The majority of the line uses the same electric multiple unit trains as the rest of BART, and shares tracks with the four other mainline services.

The 8.6-mile (13.8 km) section from Antioch to near Pittsburg/Bay Point station, known as eBART, uses diesel multiple units.

[5] On September 14, 2015, the Concord short turns were cut to Pleasant Hill to allow for increased frequency.

[7] The extra commute trains were eliminated effective March 19, 2020, due to ridership decreases caused by the COVID-19 pandemic.

[11] When the SFO/Millbrae extension opened on June 22, 2003, BART extended the Yellow Line to Millbrae but bypassed San Francisco International Airport station (SFO).

[12] In January 2008, BART re-extended the line to SFO at all times, and in September 2009, trains were further extended to Millbrae on evenings and weekends.

[13] Yellow and Purple line trains were interlined on Sundays, with no transfer required at SFO.

Trains and tracks for the portion of the Yellow Line between Antioch and Pittsburg/Bay Point are incompatible with those of the main BART rapid transit system, making it impossible for trains to move between the two systems;[28] instead, passengers transfer via a cross platform interchange at an auxiliary BART stop to the east of Pittsburg/Bay Point – the BART to Antioch platform is accessible only via an intra-station ride from the main station to this auxiliary stop.