All routes pass through Oakland, and all but the Richmond–Fremont route pass through the Transbay Tube into San Francisco and beyond to Daly City. Most segments of the BART system carry trains of more than one route.
Trains regularly operate on five routes. Unlike most other rapid transit and rail systems around the world, BART lines are generally not referred to by shorthand designations – they are only occasionally referred to officially by color names. However, future train cars will display line colors more prominently.
The five BART lines are generally identified on maps, schedules, and signage by the names of their termini
Fares on BART are comparable to those of commuter rail systems and are higher than those of most subways, especially for long trips. The fare is based on a formula that takes into account both the length and speed of the trip. A surcharge is added for trips traveling through the Transbay Tube, to Oakland International Airport, and/or through San Mateo County (which access to includes San Francisco International Airport), which is not a BART member. Passengers can use refillable paper-plastic-composite tickets, on which fares are stored via a magnetic strip, to enter and exit the system. The exit faregate prints the remaining balance on the ticket each time the passenger exits the station. A paper ticket can be refilled at a ticket machine, the remaining balance on any ticket can be applied towards the purchase of a new one, or a card is captured by the exit gate when the balance reaches zero; multiple low value cards can be combined to create a larger value card but only at specific ticket exchange locations, located at some BART stations.
BART relies on unused ticket values on discarded low-value cards for additional revenue, as much as $9.9 million. The paper ticket technology is identical to the Washington Metro's paper fare card, though the BART system does not charge higher fares during rush hour. Both systems were supplied by Cubic Transportation Systems, with contract for BART being awarded in 1974.
Clipper, a contactless smart card accepted on all major Bay Area public transit agencies, may be used in lieu of a paper ticket.
The minimum fare is $1.95 (except San Mateo County trips) under 6 miles (9.7 km). The maximum one-way fare including all possible surcharges is $15.70, the journey between San Francisco International Airport and Oakland International Airport. The farthest possible trip, from Pittsburg/Bay Point to Millbrae, costs less because of the $4 additional charge added to SFO trips and $6 additional charge added to OAK trips. Entering and exiting the same station within three hours accrues an excursion fare of $5.75. Passengers without sufficient fare to complete their journey must use a cash-only AddFare machine to pay the remaining balance in order to exit the station.
BART uses a system of five different color-coded tickets for regular fare, special fare, and discount fare to select groups as follows:
Unlike many other rapid transit systems, BART does not have an unlimited ride pass, and the only discount provided to the public is a 6.25% discount when "high value tickets" are purchased with fare values of $48 and $64, for prices of $45 and $60 respectively. Amtrak's Capitol Corridor and San Joaquins trains sell $10 BART tickets on board in the café cars for only $8, resulting in a 20% discount. A 62.5% discount is provided to seniors, the disabled, and children age 5 to 12. Middle and high school students 13 to 18 may obtain a 50% discount if their school participates in the BART program; these tickets are intended to be used only between the students' home station and the school's station and for transportation to and from school events. The tickets can be used only on weekdays. These School Tickets and BART Plus tickets have a last-ride bonus where if the remaining value is greater than $0.05, the ticket can be used one last time for a trip of any distance. Most special discounted tickets must be purchased at selected vendors and not at ticket machines. The Bart Plus tickets can be purchased at the ticket machines.
The San Francisco Muni "A" monthly pass provides unlimited rides within San Francisco, with no fare credit applied for trips outside of the City. San Francisco pays $1.02 for each trip taken under this arrangement.
Fares are enforced by the station agent, who monitors activity at the fare gates adjacent to the window and at other fare gates through closed circuit television and faregate status screens located in the agent's booth. All stations are staffed with at least one agent at all times.
Proposals to simplify the fare structure abound. A flat fare that disregards distance has been proposed, or simpler fare bands or zones. Either scheme would shift the fare-box recovery burden to the urban riders in San Francisco, Oakland and Berkeley and away from suburban riders in East Contra Costa, Southern Alameda, and San Mateo Counties, where density is lowest, and consequently, operational cost is highest.