https://techcrunch.com/2021/02/17/apple-pay-will-soon-work-on-bart-and-muni/

If you’ve ever tried to hop on the bus in San Francisco and were bummed to find that Apple Pay wasn’t an option (unlike in New York, Beijing, and plenty of other major cities): good news! That’s changing. Apple has announced that support for Clipper (the payment system for BART, Muni, Caltrain, AC Transit, and a bunch of other Bay Area transit agencies) is officially on the way. You’ll soon be able to just tap your iPhone or Apple Watch to the card reader and be on your way.

Apple says that Apple Pay will work across all 24 agencies where Clipper is accepted, meaning it should play friendly with: