The Atchison, Topeka & Santa Fe Railway (AT&SF) was chartered on February 11, 1859, to join Atchison and Topeka, Kansas, with Santa Fe, New Mexico. In its early years, the railroad opened Kansas to settlement. Much of its revenue came from wheat grown there and from cattle driven north from Texas to Wichita and Dodge City by September 1872.

Rather than turn its survey southward at Dodge City, AT&SF headed southwest over Raton Pass because of coal deposits near Trinidad, Colorado and Raton, New Mexico. The Denver & Rio Grande Railroad (D&RG) was also aiming at Raton Pass, but AT&SF crews arose early one morning in 1878 and were hard at work with picks and shovels when the D&RGW crews showed up for breakfast.

At the same time the two railroads had a series of skirmishes over occupancy of the Royal Gorge west of Cañon City, Colorado; physical confrontations led to two years of armed conflict that became known as the Royal Gorge Railroad War. Federal intervention prompted an out-of-court settlement on February 2, 1880, in the form of the so-called "Treaty of Boston", wherein D&RG was allowed to complete its line and lease it for use by Santa Fe. D&RG paid an estimated $1.4 million to Santa Fe for its work within the Gorge and agreed not to extend its line to Santa Fe, while Santa Fe agreed to forego its planned routes to Denver and Leadville.

Building across Kansas and eastern Colorado was simple, with few natural obstacles (certainly fewer than the railroad was to encounter further west), but the railroad found it almost economically impossible because of the sparse population. It set up real estate offices in the area and promoted settlement across Kansas on the land that was granted to it by Congress in 1863. It offered discounted fares to anyone who traveled west to inspect land; if the land was purchased, the railroad applied the passenger's fare toward the price of the land.

AT&SF reached Albuquerque in 1880; Santa Fe, the original destination of the railroad, found itself on a short branch from Lamy, New Mexico.

In March 1881 AT&SF connected with the Southern Pacific (SP) at Deming, New Mexico, forming the second transcontinental rail route. The railroad then built southwest from Benson, Arizona, to Nogales on the Mexican border where it connected with the Sonora Railway, which the AT&SF had built north from the Mexican port of Guaymas.

AT&SF purchased the Southern California Railway on Janurary 17, 1906, with this purchase they also acquired the Los Angeles and San Gabriel Valley Railroad and the California Central Railway.

Atlantic and Pacific Railway

The Atlantic & Pacific Railroad (A&P) was chartered in 1866 to build west from Springfield, Missouri, along the 35th parallel of latitude (approximately through Amarillo, Texas and Albuquerque, New Mexico) to a junction with SP at the Colorado River. The infant A&P had no rail connections. The line that was to become the St. Louis–San Francisco Railway (Frisco) would not reach Springfield for another four years, and SP did not build east from Mojave to the Colorado River until 1883. A&P started construction in 1868, built southwest into what would become Oklahoma, and promptly entered receivership.

In 1879 A&P struck a deal with the Santa Fe and Frisco railroads to construct a rail line for each. The railroads would jointly build and own the A&P railroad west of Albuquerque.

In 1883 A&P reached Needles, California, where it connected with an SP line. A&P also built a line between Tulsa, Oklahoma and St. Louis, Missouri for the Frisco, but the Tulsa-Albuquerque portion remained unbuilt.

Expansion

The Santa Fe began to expand: a line from Barstow, California, to San Diego in 1885 and to Los Angeles in 1887; control of the Gulf, Colorado & Santa Fe Railway (Galveston-Fort Worth) in 1886 and a line between Wichita and Fort Worth in 1887; lines from Kansas City to Chicago, from Kiowa, Kansas to Amarillo, and from Pueblo to Denver (paralleling the D&RGW) in 1888; and purchase of the Frisco and the Colorado Midland Railway in 1890. By January 1890, the entire system consisted of some 7,500 miles of track.

The Panic of 1893 had the same effect on the AT&SF that it had on many other railroads; financial problems and subsequent reorganization. In 1895 AT&SF sold the Frisco and the Colorado Midland and wrote off the losses, but it still retained control of the A&P.

The Santa Fe Railway still wanted to reach California on its own rails (it leased the SP line from Needles to Barstow), and the state of California eagerly courted the railroad to break SP's monopoly. In 1897 the railroad traded the Sonora Railway of Mexico to SP for their line between Needles and Barstow, giving AT&SF its own line from Chicago to the Pacific coast. It was unique in that regard until the Milwaukee Road completed its extension to Puget Sound in 1909.

Subsequent expansion of the Santa Fe Railway encompassed lines from Amarillo to Pecos (1899); Ash Fork, Arizona to Phoenix (1901); Williams, Arizona to the Grand Canyon (1901); the Belen Cutoff from the Pecos line at Texico to Isleta Pueblo, New Mexico, south of Albuquerque, bypassing the grades of Raton Pass (1907); and the Coleman Cutoff, from Texico to Coleman, Texas, near Brownwood (1912).

In 1907, AT&SF and SP jointly formed the Northwestern Pacific Railroad (NWP), which took over several short railroads and built new lines connecting them to form a route from San Francisco north to Eureka, California. In 1928, Santa Fe sold its half of NWP to SP. In addition, Santa Fe purchased the U.S. portion of the Kansas City, Mexico & Orient Railway (the Mexican portion of the line became the Chihuahua-Pacific Railway, now part of National Railways of Mexico).

Because long stretches of its main line traverse areas without water, Santa Fe was one of the first buyers of diesel locomotives for freight service. The railroad was known for its passenger trains, notably the Chicago-Los Angeles El Capitan and Super Chief (currently operated as Amtrak's Southwest Chief), and for the on-line eating houses and dining cars that were operated by Fred Harvey. Several of these Harvey Houses survive - most notably the El Tovar, which is positioned right alongside the Grand Canyon.

On March 29, 1955, the railway was one of many companies that sponsored attractions in Disneyland with its 5-year sponsorship of all Disneyland trains and stations.

Post-World War II construction projects included an entrance to Dallas from the north, and relocation of the main line across northern Arizona, between Seligman and Williams. In 1960, AT&SF bought the Toledo, Peoria & Western Railroad (TP&W), then sold a half interest to the Pennsylvania Railroad (PRR). TP&W cut straight east across Illinois from near Fort Madison, Iowa (Lomax, IL), to a connection with PRR at Effner, Indiana (Illinois-Indiana border), forming a bypass around Chicago for traffic moving between the two lines. The TP&W route did not mesh with the traffic pattern PRR successor Conrail developed after 1976, so AT&SF bought back the other half, merged with TP&W in 1983, then sold it back into independence in 1989.

Southern Pacific Merger

AT&SF began to propose a merger in the early 1980s. The Southern Pacific Santa Fe Railroad (SPSF) was a proposed merger between the parent companies of the Southern Pacific and AT&SF announced on December 23, 1983. As part of the joining of the two firms, all rail and non-rail assets owned by Santa Fe Industries and the Southern Pacific Transportation Company were placed under the control of a holding company, the Santa Fe–Southern Pacific Corporation. The merger was subsequently denied by the Interstate Commerce Commission (ICC) on the basis that it would create too many duplicate routes.

The companies were so confident that the merger would be approved they began repainting locomotives and non-revenue rolling stock in a new unified paint scheme. After the ICC's denial, railfans joked that SPSF really stood for "Shouldn't Paint So Fast." While Southern Pacific was sold off, all of the California real estate holdings were consolidated in a new company, Catellus Development Corporation, making it the state's largest private landowner. Some time later, Catellus would purchase the Union Pacific Railroad's interest in the Los Angeles Union Passenger Terminal (LAUPT). After SP's sale, SPSF is renamed to Santa Fe Pacific Corporation, the holding company of AT&SF.

Burlington Northern Merger

On September 22, 1995, AT&SF merged with Burlington Northern Railroad to form the Burlington Northern & Santa Fe Railway (BNSF). Some of the challenges resulting from the joining of the two companies included the establishment of a common dispatching system, the unionization of AT&SF's non-union dispatchers, and incorporating AT&SF's train identification codes throughout. The two lines maintained separate operations until December 31, 1996 when it officially became BNSF.