It operates over about 371 miles (597 km) of owned or leased track primarily on several lines in California's Central Valley/San Joaquin Valley around Fresno and Bakersfield.

One was incorporated by Leland Stanford and Associates in 1868 to build an 11.3-mile (18.2 km) line from Lathrop, California to the Stanislaus River and was consolidated in 1870 into the Central Pacific Railroad.

The second San Joaquin Valley Railroad operated from 1892 to 1893 between Fresno and Friant over 24.1 miles (38.8 km) of track and was sold at foreclosure to the Southern Pacific.

[3] This mainline route was formerly known as Southern Pacific's "West Side Line" and at one time extended from Tracy, California and then south through the West side of the San Joaquin Valley (I-5 corridor) via Patterson, Gustine, Newman, Los Banos, Oxalis and then east to Fresno via Ingle and Kerman.

The Southern Pacific constructed the track from Tracy to Newman (37 miles [60 km]) and from Los Banos to Armona (near Fresno) in 1891.

Southern Pacific's overnight Owl passenger train (#57/58) operated over this line between San Francisco and Los Angeles into 1965.

This section of track, which runs approximately 8 miles to Lindsay was pending formal abandonment whereupon the rails were expected to be immediately pulled up upon STB approval.

However the Cross Valley Corridor passenger train service is planning to upgrade the tracks to Lindsay and rebuild them to Porterville.

The Porterville-Orosi District was constructed by the Minkler Southern Railway, itself controlled by the Santa Fe through ownership of the entire capital stock.

The line ran from Minkler to Ducor, CA; south of Ducor, the ATSF ran via trackage rights on the Southern Pacific's Exeter Branch to Famoso, and then to Bakersfield on the Bakersfield Subdivision, where the line split off and entered the ATSF yard.