The Dumbarton Rail Bridge lies just to the south of the Dumbarton road bridge. Built in 1910, the rail bridge was the first structure to span San Francisco Bay, shortening the rail route between Oakland and San Francisco by 26 miles (42 km). The last freight train traveled over the bridge in 1982, and it has been proposed since 1991 to reactivate passenger train service to relieve traffic on the road bridges, though this would entail a complete replacement of the existing bridge. Part of the western timber trestle approach collapsed in a suspected arson fire in 1998.

Caltrain is a California commuter rail line serving the San Francisco Peninsula and Santa Clara Valley. The southern terminus is in San Jose at Tamien station with weekday rush hour service running as far as Gilroy. The northern terminus of the line is in San Francisco at 4th and King Street. Caltrain has 28 regular stops, one limited-service weekday-only stop, one weekend-only stop (Broadway), and one football-only stop (Stanford). While average weekday ridership in 2019 exceeded 63,000, impacts of the COVID-19 pandemic have been significant: in August 2022, Caltrain had an average weekday ridership of 18,600 passengers.