The struggle between the city of Modesto and the railroad over a new depot had gone on since as early as 1909. Finally, in 1914, the Modesto Chamber of Commerce filed a complaint with the California Railroad Commission that ruled in favor of the chamber and ordered the railroad to build a new depot. The commission suggested one in the Mission style popular at the time.
The railroad relied on its own architect and assistant chief engineer John Quincy Barlow and his team to design the depot. Construction began 12 July 1915, and the depot opened for service at 4 pm, 11 December 1915. Southern Pacific Railroad used the depot until 1971 when it ended passenger service to Modesto. In 1992, the depot was converted into a transportation center for city and regional bus service. Plans are to renovate the depot 2020 for passengers using the ACE Train service to San Jose and Merced.