Before November 12, 1999, trains stopped instead in Riverbank, about 4 miles north.

[2][5] In the past trains also stopped at the Modesto Transportation Center, which was built by the Southern Pacific Transportation Company in 1915, and in the future rail service will move there again when the Altamont Corridor Express begins service to Modesto.

[6] In October 2024, the state was awarded a $18.7 million federal grant to build a second platform at Modesto and Denair stations.

[7] Modesto is the point where the San Joaquin splits, with trains bound for the Bay Area continuing to Stockton's San Joaquin Street station and trains heading to Sacramento continuing to Stockton–Downtown station.

Media related to Modesto station at Wikimedia Commons