It was formed in 1903 as an attempt to break the near-monopoly the Southern Pacific Railroad had on rail service into northern California.

The Western Pacific Railway acquired the Alameda and San Joaquin Railroad and began construction on what became known as the Feather River Route.

This route, today part of BNSF's Gateway Subdivision, 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 Great Depression and had to be reorganized.

The WP handled the "Silver Lady" from Oakland, California, to Salt Lake City, Utah from 1949 to 1970.