The Northern Pacific was chartered on July 2, 1864 as the first northern transcontinental railroad in the United States. It was granted some 47,000,000 acres of land in exchange for building rail transportation to an undeveloped territory. Josiah Perham (for whom Perham, Minnesota is named) was elected its first president on December 7, 1864.

For the next six years, backers of the road struggled to find financing. Though John Gregory Smith succeeded Perham as president on January 5, 1866, groundbreaking did not take place until February 15, 1870, at Thompson Junction, Minnesota, 25 miles west of Duluth, Minnesota. The backing and promotions of famed Civil War financier Jay Cooke in the summer of 1870 brought the first real momentum to the company.

Over the course of 1870, the Northern Pacific pushed westward from Minnesota into present-day North Dakota. It also began reaching from Kalama, Washington Territory, on the Columbia River outside of Portland, Oregon, towards Puget Sound. Four small construction engines were purchased, the Minnetonka, Itaska, Ottertail and St. Cloud, the first of which was shipped to Kalama by ship around Cape Horn. In Minnesota, the Lake Superior and Mississippi Railroad completed construction of its 155 mile line stretching from St. Paul, Minnesota, to Lake Superior at Duluth in 1870. It was leased to the Northern Pacific the following year, and was eventually absorbed by the Northern Pacific.

In 1871, Northern Pacific completed some 230 miles of railroad on the east end of its system, reaching out to Moorhead, Minnesota, on the North Dakota border. In the west, the track extended 25 miles north from Kalama. Surveys were carried out in North Dakota protected by 600 troops from General Winfield Scott Hancock. Headquarters and shops were established in Brainerd, Minnesota, a town named for the President John Gregory Smith's wife Anna Elizabeth Brainerd.

In 1872, the company put down 164 miles of main line across North Dakota, with an additional 45 miles in Washington. On November 1, General George Washington Cass became the third president of the company. Cass had been a vice-president and director of the Pennsylvania Railroad, and would lead the Northern Pacific through some of its most difficult times.

Attacks on survey parties and construction crews building into Native American homelands in North Dakota became so prevalent the company appealed for Army protection from President Ulysses S. Grant. In 1872 the Northern Pacific also opened colonization offices in Europe, seeking to attract settlers to the sparsely populated and undeveloped region it served. Survey parties accompanied by Federal troops, railroad construction, permanent settlement and development, along with the discovery of gold in nearby South Dakota, all served as a backdrop leading up to the Battle of the Little Bighorn and the defeat of General George Armstrong Custer in 1876.

In 1873, Northern Pacific made impressive strides before a terrible stumble. Rails from the east reached the Missouri River on June 4. After several years of study, Tacoma, Washington, was selected as the road's western terminus on July 14. However, for the past three years the financial house of Jay Cooke and Company had been throwing money into the construction of the Northern Pacific. Like many western transcontinentals, the staggering costs of building a railroad into a vast wilderness were drastically underestimated. For a variety of reasons, led by the costs of constructing the railroad itself, Cooke and Company closed its doors on September 18. Soon, the Panic of 1873 engulfed the United States, ushering in a severe recession which would drag on for several years. The Northern Pacific, however, survived bankruptcy that year, due to austerity measures put in place by President Cass. In fact, working with last-minute loans from Director John Commiger Ainsworth of Portland, the Northern Pacific completed the line from Kalama to Tacoma, 110 miles, before the end of the year. On December 16, the first steam train arrived in Tacoma. The year of 1874, however, found the company moribund.

Northern Pacific slipped into its first bankruptcy on June 30, 1875. Cass resigned to become receiver of the company, and Charles Barstow Wright became fourth president of the company. Frederick Billings, namesake of Billings, Montana, formulated a reorganization plan which was put into effect. This same year George Custer was assigned to Fort Rice, Dakota Territory, and charged with protecting railroad survey and construction crews.

In 1877, construction resumed in a small way. Northern Pacific pushed a branch line southeast from Tacoma to Puyallup, Washington and on to the coal fields around Wilkeson, Washington. Much of the coal was destined for export through Tacoma to San Francisco, California, where it would be thrown into the fireboxes of Central Pacific Railroad steam engines. This small amount of construction was one of the largest projects the company would undertake in the years between 1874 and 1880. That same year the company built a large shop complex at South Tacoma, Washington. For many years the shops at Brainerd and South Tacoma would carry out heavy repairs and build equipment for the railroad.

On May 24, 1879, Vermont lawyer Frederick Billings became the president of the company. Billings' tenure would be short but ferocious. Reorganization, bond sales, and improvement in the U.S. economy allowed Northern Pacific to strike out across the Missouri River by letting a contract to build 100 miles of railroad west of the river. The railroad's new-found strength, however, would be seen as a threat in certain quarters.

Ferdinand Heinrich Gustav Hilgard had been born in Bavaria in 1835, emigrating to America in 1853, at the ripe old age of 18. Settling in Illinois, the well-educated Hilgard became a journalist and editor, covering the Lincoln-Douglas debates, then the American Civil War for the larger New York papers, changing his name to Henry Villard along the way. He went back to his native Germany in 1871, where he came in contact with European financial interests speculating in American railroads. When he returned to the United States after the Panic of 1873, he was the representative of these concerns. In the few short years prior to 1880, Villard intervened on the behalf of these interests in several transportation systems in Oregon. Through Villard's work, most of these lines wound up in the hands of the European creditors' holding company, the Oregon and Transcontinental.

Of the lines held by the Oregon and Transcontinental, the most important was the Oregon Railway and Navigation Company, a line running east from Portland along the south bank of the Columbia River to a connection with the Union Pacific Railroad's Oregon Short Line at the confluence of the Columbia River and the Snake River near Wallula, Washington. Within a decade of his return, Henry Villard became the head of a transportation empire in the Pacific Northwest that had but one real competitor, the ever-expanding Northern Pacific. Northern Pacific's completion threatened the holdings of Villard in the Northwest, and especially in Portland. Portland would become a second-class city if the Puget Sound ports at Tacoma and Seattle, Washington were connected to the East by rail. Villard, who had been building a monopoly of river and rail transportation in Oregon for several years, now launched a daring raid. Using his European connections and a reputation for having "bested" Jay Gould in a battle for control of the Kansas Pacific years before, Villard solicited — and raised — $8 million from his associates. This was his famous "Blind Pool," Villard's associates were not told what the money would be used for. In this case, the funds were used to purchase control of the Northern Pacific. Despite a tough fight, Billings and his backers were forced to capitulate; he resigned the presidency June 9. Ashabel H. Barney was brought in as an interim caretaker of the railroad from June 19 to September 15, when Villard was finally elected president by the stockholders. For the next two years, Villard and the Northern Pacific rode the whirlwind.

In 1882, 360 miles of main line and 368 miles of branch line were completed, bringing totals to 1,347 miles and 731 miles, respectively. On October 10, 1882, the line from Wadena, Minnesota, to Fergus Falls, Minnesota, opened for service. The Missouri River was bridged with a million-dollar span on October 21, 1882. The Missouri had been handled by a ferry service most of the year. During winters, when ice was thick enough, the rails were laid across the river itself. General Herman Haupt another veteran of the Civil War and the Pennsylvania Railroad, set up the Northern Pacific Beneficial Association on August 19. A forerunner of the modern health maintenance organization, the NPBA ultimately established a series of four hospitals across the system in St. Paul, Minnesota, Glendive, Montana, Missoula, Montana, and Tacoma, Washington, to care for employees, retirees, and their families.

Events reached their climax in 1883. On January 15th, the first train reached Livingston, Montana, at the eastern foot of Bozeman Pass. Livingston, like Brainerd and South Tacoma before it, would grow to encompass a large backshop handling heavy repairs for the railroad. It would also mark the east-west dividing line on the Northern Pacific system. Villard pushed hard for the completion of the Northern Pacific in 1883. During Villard's presidency, crews were averaging a mile and half of track laying each day. Finally, in September, the line neared completion. To celebrate, Villard chartered four trains to carry visitors from the East to Gold Creek in central Montana. No expense was spared and the list of dignitaries included Frederick Billings, Ulysses S. Grant, and Villard's in-laws, the family of abolitionist William Lloyd Garrison. On September 8, the Gold Spike was driven at Gold Creek.

However, Villard's fall turned out to be even swifter than his ascendancy. Like Jay Cooke, the enormous costs of constructing the railroad now consumed him. Wall Street bears attacked the stock shortly after the Gold Spike, after the realization that the Northern Pacific was a very long road with very little business. Villard himself is said to have suffered a nervous breakdown in the days following the Gold Spike, and he left the presidency of the Northern Pacific and the United States to convalesce in Germany in January, 1884. Again, the presidency of the Northern Pacific was handed to a professional railroader, Robert Harris, former head of the Chicago, Burlington and Quincy Railroad. For the next four years, until the return of the Villard clique, Harris worked at improving the property and breaking away from its tangled relationship with the Oregon Railway and Navigation Company.

Throughout the middle 1880s, the Northern Pacific pushed to reach Puget Sound directly, rather than a roundabout route following the Columbia River. Surveys of the Cascade Mountains, carried out intermittently since the 1870s, now began anew. Virgil Gay Bogue, a veteran civil engineer, was sent to explore the Cascades again. On March 19, 1881, he discovered Stampede Pass. In 1884, after the departure of Villard, the Northern Pacific began building toward Stampede Pass from Wallula in the east and the area of Wilkeson in the west. By the end of the year, rails had reached Yakima, Washington in the east. A 77 mile gap remained in 1886. In January of that year, Nelson Bennett was given a contract to construct a 9,850 foot tunnel under Stampede Pass. The contract specified a short amount of time for completion, and a large penalty if the deadline were missed. While crews worked on the tunnel, the railroad built a temporary switchback route across the pass. With numerous timber trestles and grades which approached six percent, the temporary line required the two largest locomotives in the world (at that time) to handle a tiny five-car train. On May 3, 1888 crews holed through the tunnel, and on May 27th, the first train direct to Puget Sound passed through.

Despite this success, the Northern Pacific, like many U.S. roads, was living on borrowed time. From 1887 until 1893 Henry Villard returned to the board of directors. Though offered the presidency, he refused. However, an associate of Villard dating back to his time on the Kansas Pacific, Thomas Fletcher Oakes, assumed the presidency on September 20, 1888. In an effort to garner business, the Villard regime pursued an aggressive policy of branch line expansion. In addition, the Northern Pacific experienced the first competition in the form of James Jerome Hill and his Great Northern Railway. The Great Northern, like the Northern Pacific before it, was pushing west from the Twin Cities towards Puget Sound, and would be completed in 1893. To combat the Great Northern, in a few instances Villard built branch line mileage simply to occupy a territory, regardless of whether the territory offered the railroad any business. Mismanagement, sparse traffic, and the Panic of 1893 sounded the death knell for the Northern Pacific and Villard's interest in railroading. The company slipped into its second bankruptcy on October 20, 1893.

Oakes was named receiver and Brayton C. Ives, a former chairman of the New York Stock Exchange became president. For the next three years, the Villard-Oakes interests and the Ives interest feuded for control of the Northern Pacific. Oakes was eventually forced out as receiver, but not before three separate courts were claiming jurisdiction over the Northern Pacific's bankruptcy. Things came to a head in 1896, when first Edward D. Adams was appointed president, then less than two months later, Edwin Winter. Ultimately, the task of straightening out the muddle of the Northern Pacific was John Pierpont Morgan. Morganization of the Northern Pacific, a process which befell many U.S. roads in the wake of the Panic of 1893, was handed to Morgan lieutenant Charles Henry Coster. The new president, beginning September 1, 1897, was Charles Sanger Mellen. Though James J. Hill had purchased an interest in the Northern Pacific during the troubled days of 1896, Coster and Mellen would advocate, and follow, a staunchly independent line for the Northern Pacific for the next four years. Only the early death of Coster from overwork, and the promotion of Mellen to head the Morgan-controlled New York, New Haven and Hartford Railroad in 1903, would bring the Northern Pacific closer to the orbit of James J. Hill.

Despite this success, the Northern Pacific, like many U.S. roads, was living on borrowed time. From 1887 until 1893 Henry Villard returned to the board of directors. Though offered the presidency, he refused. However, an associate of Villard dating back to his time on the Kansas Pacific, Thomas Fletcher Oakes, assumed the presidency on September 20, 1888. In an effort to garner business, the Villard regime pursued an aggressive policy of branch line expansion. In addition, the Northern Pacific experienced the first competition in the form of James Jerome Hill and his Great Northern Railway. The Great Northern, like the Northern Pacific before it, was pushing west from the Twin Cities towards Puget Sound, and would be completed in 1893. To combat the Great Northern, in a few instances Villard built branch line mileage simply to occupy a territory, regardless of whether the territory offered the railroad any business. Mismanagement, sparse traffic, and the Panic of 1893 sounded the death knell for the Northern Pacific and Villard's interest in railroading. The company slipped into its second bankruptcy on October 20, 1893. Oakes was named receiver and Brayton C. Ives, a former chairman of the New York Stock Exchange became president. For the next three years, the Villard-Oakes interests and the Ives interest feuded for control of the Northern Pacific.

Oakes was eventually forced out as receiver, but not before three separate courts were claiming jurisdiction over the Northern Pacific's bankruptcy. Things came to a head in 1896, when first Edward D. Adams was appointed president, then less than two months later, Edwin Winter. Ultimately, the task of straightening out the muddle of the Northern Pacific was John Pierpont Morgan. Morganization of the Northern Pacific, a process which befell many U.S. roads in the wake of the Panic of 1893, was handed to Morgan lieutenant Charles Henry Coster. The new president, beginning September 1, 1897, was Charles Sanger Mellen. Though James J. Hill had purchased an interest in the Northern Pacific during the troubled days of 1896, Coster and Mellen would advocate, and follow, a staunchly independent line for the Northern Pacific for the next four years. Only the early death of Coster from overwork, and the promotion of Mellen to head the Morgan-controlled New York, New Haven and Hartford Railroad in 1903, would bring the Northern Pacific closer to the orbit of James J. Hill.

In the late 1880s, the Villard regime, in another one of its costly missteps, attempted to stretch the Northern Pacific from the Twin Cities to the all-important rail hub of Chicago, Illinois. A costly project was begun in creating a union station and terminal facilities for a Northern Pacific which had yet to arrive. Rather than build directly down to Chicago, perhaps following the Mississippi River as the Chicago, Burlington and Quincy had done, Villard chose to lease the Wisconsin Central. Some backers of the Wisconsin Central had long associations with Villard, and an expensive lease was worked out between the two companies which was only undone by the Northern Pacific's second bankruptcy. The ultimate result was that the Northern Pacific was left without a direct connection to Chicago, the primary interchange point for most of the large U.S. railroads. Fortunately, the Northern Pacific was not alone. James J. Hill, controller of the Great Northern, which was completed between the Twin Cities and Puget Sound in 1893, also lacked a direct connection to Chicago. Hill went looking for a road with an existing route between the Twin Cities and Chicago which could be rolled into his holdings and give him a stable path to that important interchange. At the same time, Edward Henry Harriman, head of the Union Pacific Railroad, was also looking for a road which could connect his company to Chicago. The road both Harriman and Hill looked at was the Chicago, Burlington and Quincy. To Harriman, the Burlington was a road which paralleled much of his own, and offered tantalizing direct access to Chicago. For Hill as well there was the possibility of a high-speed link directly with Chicago.

Though the Burlington did not parallel the Great Northern or the Northern Pacific, it would give them a powerful railroad in the central West. Harriman was the first to approach the Burlington's aging chieftain, the irascible Charles Elliott Perkins. The price for control of the Burlington, as set by Perkins, was $200 a share, more than Harriman was willing to pay. Hill, however, met the price, and control of the Burlington was divided equally at about 48.5 percent each between the Great Northern and the Northern Pacific. Not to be outdone, Harriman now came up with a crafty plan: Buy a controlling interest in the Northern Pacific and use its power on the Burlington to place friendly directors upon its board. On May 3, 1901, Harriman began his stock raid which would become known as the Northern Pacific Corner. By the end of the day he was short just 40,000 shares of common stock. Harriman placed an order to cover this, but was overridden by his broker, Jacob Schiff, of Kuhn, Loeb & Co. Hill, on the other hand, reached the vacationing Morgan in Italy and managed to place an order for 150,000 shares of common stock. Though Harriman might be able to control the preferred stock, Hill knew the company bylaws allowed for the holders of the common stock to vote to retire the preferred. In three days, however, the Harriman-Hill imbroglio managed to wreak havoc on the stock market. Northern Pacific stock was quoted at $150 a share on May 6, and is reported to have traded as much as $1,000 a share behind the scenes. Harriman and Hill now worked to settle the issue for brokers to avoid panic. Hill, for his part, attempted to avoid future stock raids by placing his holdings in the Northern Securities Company, a move which would be undone by the Supreme Court in 1904 under the auspices of the Sherman Anti-Trust Act. Harriman was not immune either; he was forced to break up his holdings in the Union Pacific and the Southern Pacific Railroad a few years later.

In 1903, Hill finally got his way with the House of Morgan. Howard Elliott, another veteran of the Chicago, Burlington and Quincy, became president of the Northern Pacific on October 23. Elliott was a relative of the Burlington's crusty chieftain Charles Elliott Perkins, and more distantly the Burlington's great backer, John Murray Forbes. He had spent twenty years in the trenches of Midwest railroading, where rebates, pooling, expansion and rate wars had brought ruinous competition. Having seen the effects of having multiple railroads attempt to serve the same destination, he was very much in tune with James J. Hill's philosophy of "community of interest," a loose affiliation or collusion among roads in an attempt to avoid duplicating routes, rate wars, weak finances and ultimately bankruptcies and reorganizations. Elliott would be left to make peace with the Hill-controlled Great Northern; the Harriman-controlled Union Pacific; and, between 1907 and 1909, the last of the northern transcontinentals, the Chicago, Milwaukee, St. Paul and Pacific Railroad, more commonly known as the Milwaukee Road.

In later years, consolidation in American railroading brought the Northern Pacific together with the Burlington, the Great Northern, and the Spokane, Portland and Seattle Railway on March 2, 1970 to form the Burlington Northern Railroad. Ironically, the merger was allowed despite a challenge in the Supreme Court, essentially reversing the outcome of the 1904 Northern Securities ruling.

The North Coast Limited was a famous passenger train operated by the Northern Pacific Railway between Chicago and Seattle via Bismarck, North Dakota. It commenced service on April 29, 1900, served briefly as a Burlington Northern train after the merger on March 2, 1970 and ceased operation the day before Amtrak began service (April 30, 1971). The Chicago Union Station to Minneapolis leg of the train's route was operated by the Chicago Burlington and Quincy railroad along its Mississippi River mainline through Wisconsin.

In the mid 1970s, the North Coast Limited service was restarted by Amtrak as the North Coast Hiawatha operating via the Milwaukee Road mainline between Chicago and Minneapolis. The train continued running on a 3 day a week schedule until it was again discontinued in 1979.

The North Coast Limited was the Northern Pacific's flagship train and the Northern Pacific itself was built along the trail first blazed by Lewis and Clark.

Presidents of Northern Pacific Railway were:

Josiah Perham, 1864-1866
John Gregory Smith, 1866-18
George Washington Cass, 1872-1875
Charles Barstow Wright, 1875-1879
Frederick Billings, 1879-1881
Henry Villard, 1881-1884
Robert Harris, 1884-1888
Thomas Fletcher Oakes, 1888-1893
Brayton C. Ives, 1893-1896
Edward Dean Adams, 1896
Edwin Winter, 1896
Charles Sanger Mellen, 1897-1903
Howard Elliott, 1903-1913
Jule Murat Hannaford, 1913-1920
Charles Donnelly, 1920-1939
Charles Eugene Denney, 1939-1950
Robert Stetson Macfarlane, 1951-1966
Louis W. Menk, 1966-1970.