[3] Amtrak Thruway routes are timed to meet trains and offer connections to points in Southern California (including Los Angeles Union Station where passengers can continue their journey on the Pacific Surfliner or Amtrak's long-distance trains), the city of San Francisco, the Central Coast, the North Coast, the High Desert (including Las Vegas), Redding, Reno, and the Yosemite Valley.

The San Joaquin Joint Powers Authority (SJJPA) is governed by a board that includes two elected representatives from each of eight counties the train travels through.

The California Department of Transportation (Caltrans) provides the funding to operate the service and also owns the rolling stock.

[4] In April 1965, as ridership on passenger trains continued to drop, the Santa Fe Railway received permission from the Interstate Commerce Commission to severely curtail Golden Gate operations, with service finally abandoned three years later.

[10] The schedule was changed on July 19, 1979, with an earlier northbound and later southbound departure, allowing single-day round trips to the Bay Area.

[11] In 1979 Amtrak proposed discontinuing the San Joaquin as part of system-wide reductions ordered by the Carter administration.

The state of California stepped in to provide a yearly subsidy of (then) $700,000 ($2.94 million adjusted for inflation) to cover the train's operating losses, and it was retained.

The state asked Amtrak to add a second round-trip between Oakland and Bakersfield and to extend the service south over the Tehachapi Pass to Los Angeles.

[22] On September 29, 2012, Governor Jerry Brown signed Assembly Bill 1779, which enabled regional government agencies to form the San Joaquin Joint Powers Authority (SJJPA) to assume administration and management of the route, while the state of California would continue to fund operations.

[23] Under the joint powers authority model, the service would be governed by a board composed of eight elected officials, appointed by an agency in each of the counties the train travels through.

[17]: 15 Two years later, the SJJPA established an early-morning "Morning Express Service" between Fresno and Sacramento, allowing same-day trips to the state capitol for the first time, was expected to result in increased ridership from business travelers.

[24] The service began on May 7, 2018, but proved to be unpopular, with ridership counts showing an average of just 50 people on the train, compared to 130 with the old timetable.

[28] As of 2020[update] the agency is increasing capacity on its routes to avoid conflicts with freight trains and add additional trips as well as plan for connections to the California High-Speed Rail system.

[32][30]: 25 When the Valley Rail project is complete, ACE will share the route to Natomas from Stockton and add an additional branch south to Ceres in 2023 with an extension to Merced in 2027.

[30]: 40 In December 2023, the Federal Railroad Administration accepted an application by Caltrans to enter the San Joaquins route into its Corridor Identification and Development Program.

[37] In 2024, the Butte County Association of Governments released a Strategic plan, named North Valley Rail to extend The San Joaquins service to Chico.

[60] Amtrak reequipped the San Joaquin trains again in 1989, this time with new Horizon coaches, when service expanded to three daily round-trips.

[64][65] The San Joaquins and Capitol Corridor share a combined fleet of 13 EMD F59PHI and ten Siemens Charger SC-44 locomotives.

[64] The Charger locomotives meet EPA Tier IV emission standards and are capable of operating at 125 mph in revenue service.

[64]Increasing ridership on the San Joaquins service led Caltrans to purchase 14 Comet IB rail cars from New Jersey Transit in 2008 for $75,000 each.

The former commuter cars were refurbished and reconfigured by Amtrak's Beech Grove Shops to serve as intercity coaches at a cost of approximately $20 million.

[67] Caltrans had planned to use the Comet Car trainsets on trains starting in July 2013, but the refurbishing process took longer than expected.

[63] The Comet Cars have major limitations for San Joaquins service, such as their manually-operated doors, which slow down boarding.

In this use, the Comet Cars do not carry passengers, and serve to meet a minimum train length requirement imposed by BNSF.

[64] San Joaquins trains are required to have a minimum of 28 axles to protect against track circuit malfunctions, an issue known as "loss of shunt."

[64] In November 2017, the California Department of Transportation announced that it would be ordering seven Siemens Venture trainsets through its contractor Sumitomo Corporation.

[64] Like the earlier bi-level cars, the Venture trainsets have doors that can operated remotely on either side of the train from a single point of control.

The first trainset was supposed to go into revenue service in 2020,[73] though Caltrans only began accepting deliveries of the new rolling stock in late 2022.