As part of the BART SFO Extension, a new intermodal terminal for BART, Caltrain, and Samtrans was built in Millbrae just north of Millbrae Avenue.
BART service to the $70 million facility began on June 22, 2003.
The station was initially served by the Pittsburg/Bay Point line, plus a shuttle service to San Francisco International Airport station (SFIA).
The shuttle service was discontinued on February 9, 2004.
The Richmond line began serving Millbrae at weekday peak hours, with the Pittsburg/Bay Point line providing service at other times.

BART service to stations in San Mateo County is funded by SamTrans, rather than county tax revenues.
As ridership stayed below expectations, SamTrans had to pay a larger-than-planned operating subsidy to BART.
On September 12, 2005, in order to lower these subsidies, BART reduced service so that only the Dublin/Pleasanton line served SFIA and Millbrae stations.
SamTrans and BART reached an agreement in February 2007 in which SamTrans would transfer control and financial responsibility of the SFO/Millbrae extension to BART, in return for BART receiving additional fixed funding from SamTrans and other sources.

On January 1, 2008, BART increased service to the San Mateo stations.
Service to Millbrae station was provided by the Richmond line on weekdays, and the Dublin/Pleasanton line on weeknights and weekends.
Direct service between SFIA and Millbrae was discontinued.
On September 14, 2009, the Pittsburg/Bay Point line was extended to Millbrae on nights and weekends (with the Dublin/Pleasanton line cut back to Daly City station), restoring direct service at those times.
On February 11, 2019, SFO–Millbrae line service resumed on weekdays and Sundays.
The station continues to be served by the Richmond line on weekdays, with the Antioch line (formerly the Pittsburg/Bay Point line) serving both SFIA and Millbrae on weeknights and Saturdays.
On February 10, 2020, the SFO–Millbrae line begna running during all operating hours, with the Antioch line operating only to SFIA.

Millbrae station was expected to have some 16,500 daily BART boardings by 2017, but has consistently fallen well short of projections, with under 7,000 daily boardings by then.

Caltrain no longer needed the historic station building after operations moved to the modern station.
The Millbrae Historical Society negotiated with Caltrain to use the building as a museum in exchange for maintaining it.
The Millbrae Train Museum opened in October 2004.
In 2006, Pullman car Civic Center, built in 1941 for the City of San Francisco, was moved adjacent to the station and opened as an exhibit.
The Society plans to acquire a locomotive and construct a section of track to run excursion service.
As part of the BART SFO Extension, a new intermodal terminal for BART, Caltrain, and Samtrans was built in Millbrae just north of Millbrae Avenue. BART service to the $70 million facility began on June 22, 2003. The station was initially served by the Pittsburg/Bay Point line, plus a shuttle service to San Francisco International Airport station (SFIA). The shuttle service was discontinued on February 9, 2004. The Richmond line began serving Millbrae at weekday peak hours, with the Pittsburg/Bay Point line providing service at other times.
BART service to stations in San Mateo County is funded by SamTrans, rather than county tax revenues. As ridership stayed below expectations, SamTrans had to pay a larger-than-planned operating subsidy to BART. On September 12, 2005, in order to lower these subsidies, BART reduced service so that only the Dublin/Pleasanton line served SFIA and Millbrae stations. SamTrans and BART reached an agreement in February 2007 in which SamTrans would transfer control and financial responsibility of the SFO/Millbrae extension to BART, in return for BART receiving additional fixed funding from SamTrans and other sources.
On January 1, 2008, BART increased service to the San Mateo stations. Service to Millbrae station was provided by the Richmond line on weekdays, and the Dublin/Pleasanton line on weeknights and weekends. Direct service between SFIA and Millbrae was discontinued. On September 14, 2009, the Pittsburg/Bay Point line was extended to Millbrae on nights and weekends (with the Dublin/Pleasanton line cut back to Daly City station), restoring direct service at those times. On February 11, 2019, SFO–Millbrae line service resumed on weekdays and Sundays. The station continues to be served by the Richmond line on weekdays, with the Antioch line (formerly the Pittsburg/Bay Point line) serving both SFIA and Millbrae on weeknights and Saturdays. On February 10, 2020, the SFO–Millbrae line begna running during all operating hours, with the Antioch line operating only to SFIA.
Millbrae station was expected to have some 16,500 daily BART boardings by 2017, but has consistently fallen well short of projections, with under 7,000 daily boardings by then.
Caltrain no longer needed the historic station building after operations moved to the modern station. The Millbrae Historical Society negotiated with Caltrain to use the building as a museum in exchange for maintaining it. The Millbrae Train Museum opened in October 2004. In 2006, Pullman car Civic Center, built in 1941 for the City of San Francisco, was moved adjacent to the station and opened as an exhibit. The Society plans to acquire a locomotive and construct a section of track to run excursion service.
Millbrae station