Rail service to the area began in 1869, when the Central Pacific Railroad established a depot where the present station stands.

Local landowning families had donated the site of the town eventually known as Lodi to the railroad as an incentive to build there.

[5] In 1993, Amtrak studied the possibility of reopening stops in California's Central Valley, and interest grew in restoring Lodi station.

The $2.3 million project involved moving the 1907 railroad building to its present location on South Sacramento Street to accommodate a new passenger platform, and additions including bus bays, a waiting room, a clock tower, and a Gateway Arch.

[5] Rail service was temporarily suspended between March 2020 and October 2021 due to the COVID-19 pandemic.