The original Western Pacific Railroad was established in 1865 to build the westernmost portion of the Transcontinental Railroad between San Jose, California (later Oakland, California), and Sacramento, California. This company was absorbed into the Central Pacific Railroad in 1870. The second company to use the name Western Pacific Railroad was founded in 1903. Under the direction of George Jay Gould I, the Western Pacific was founded to provide a standard gauge track connection to the Pacific Coast for his aspiring Gould transcontinental system.

The construction was financed by the Denver and Rio Grande Western Railroad, a company in the Gould system, which lost access to California due to the attempted acquisition of the Southern Pacific Railroad by the Rio Grande's main rival, the Union Pacific Railroad. The Western Pacific Railroad acquired the Alameda and San Joaquin Railroad and began construction on what would become the Feather River Route. In 1909 it became the last major railroad completed into California. It used 85-lb rail on untreated ties, with no tie plates except on curves over one degree; in 1935 more than half of the main line still had its original rail, most of it having carried 150 million gross tons.

In 1931 Western Pacific opened a main line north from the Feather River Canyon to the Great Northern Railway in northern California. This route, the "Highline", joined the Oakland – Salt Lake City main line at the Keddie Wye, a unique combination of two steel trestles and a tunnel forming a triangle of intersecting track. In 1935, the railroad went bankrupt because of decreased freight and passenger traffic caused by the Depression and had to be reorganized.