[6][7] During the first months of revenue service, the Automatic Train Control (ATC) system had safety problems with its design and operation.

[8] The incident drew national and international attention, followed a month later by release of the "Post Report" on BART safety by the legislative analyst for the California State Senate.

[14] The Santa Clara County Transit District – later Santa Clara Valley Transportation Authority (VTA) – bus service began operating Fremont station—San Jose service on June 25, 1973, connecting BART with the South Bay transit system.

The work included a 2,200-square-foot (200 m2) expansion of the fare lobby, new faregates, a bus transfer plaza, and a new access road.

[29] The paved lot opened in October 29, 1978, leaving the station with 1,000 parking spaces; construction of the new entrance began at that time.

[31] In April 1981, BART opened bidding for construction of an additional parking lot off Mowry Avenue on the north side of the station.

[43][44] However, the BART extension did not open until June 13, 2020, leaving Warm Springs/South Fremont as the only connecting point between the two systems until that time.

[44] As of 2024[update], BART anticipates soliciting developer proposals by 2028 for transit-oriented development to replace surface parking lots at the station..[45] A three-lane bus plaza on the east side of Fremont station is a transfer hub for AC Transit buses:[46] Two Stanford Marguerite Shuttle routes, AE-F and East Bay Express, also terminate at Fremont.