Caltrain implements a virtual fare gate system in some ways similar to BART. At BART, riders using a Clipper card tag on and off each time at the fare gate. When exiting the system, a proper fare is deducted. Caltrain is treating Clipper no different than BART, except that the stations don’t have any real fare gate.

To ensure that riders don’t cheat in the virtual fare gate system, conductors check passengers periodically to see whether their Clipper card has been tag on before boarding. Also, at the first tag, passengers are charged the maximum available fare so that Caltrain won’t lose revenue if riders neglected to tag off.

San Francisco Bay Ferry also implements the same system for its ferry routes.