There were two former San Joaquin Valley Railroads. 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 1892–1893 between Fresno and Friant over 24.1 miles (38.8 km) of track and was sold at foreclosure to the Southern Pacific.
In 1991, the SJVR operated the entire former SP line from Fresno to Famoso, but a portion north of Famoso was later abandoned.
SJVR interchanges with the BNSF Railway at Fresno and Bakersfield and with the Union Pacific at Fresno and Goshen Junction.
SJVR was originally owned by Kyle Railways. In 1992, the SJVR was created to obtain and operate several branch lines from the Southern Pacific. From 1992–1997, the SJVR was owned by Kyle Railways. In 1997, SJVR's parent, Kyle Railways, was sold to States Rail. In 2002 SJVR's new parent, States Rail, was purchased by RailAmerica. Genesee & Wyoming Inc. controlled RailAmerica in December 2012. Today the SJVR remains a shortline within the Genesee & Wyoming family of railroads.
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. California Northern Railroad now operates the northern section of the line from Tracy - Los Banos. SJVR operates the southern section of the line from Oxalis to Fresno and was at one time owned by Port Railroads, Inc. (PRI; also a Kyle subsidiary) and operated by the SJVR. On April 24, 1996 the PRI was merged into the SJVR. Both the PRI and SJVR were already Kyle Railway subsidiaries. The section of track between Los Banos and Oxalis was abandoned by Southern Pacific in 1993 and the tracks were removed soon after.
The Southern Pacific constructed the track from Tracy to Newman (37 miles) 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.
In 2008, the Surface Transportation Board approved the abandonment of the section of track between Strathmore and Jovista. This left the communities of Strathmore, Porterville, Terra Bella, Ducor, and Richgrove without any rail service. Tulare County has recently broken off negotiations with the SJVR to purchase this section of track to preserve it for future use and possible reactivation. However, beginning in September 2010, the tracks were being removed by the SJVR and the job was completed with the entire line having been pulled up in mid November. The future of this line is very much in doubt and with the rails having now been removed, it's extremely unlikely that trains will ever traverse that corridor again. As of March 2015, the SJVR has embargoed the line with the rails spiked at the south end of Exeter with some crossing signals south already having been partially dismantled. This section of track, which runs approximately 8 miles to Lindsay is now pending formal abandonment whereupon the rails are expected to be immediately pulled up upon STB approval. The sections from Exeter to Dinuba along with former ATSF track between Lindsay and Exeter were expected to follow given their poor condition and lack of use.