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The MBTA has various fare structures for its various types of service. The plastic CharlieCard electronic farecard is accepted only on the subway and bus systems. Commuter rail and ferry accept paper CharlieTickets and the mTicket mobile app. Only buses, surface trolleys, and Commuter Rail accept cash on board, which is discouraged (with a $3 fee for Commuter Rail for stations with fare vending machines). Passengers pay for subway and bus rides at faregates in station entrances or fareboxes in the front of vehicles; MBTA employees manually check tickets on the commuter rail and ferries. For paratransit service, instead of physical fare media passengers maintain an account to which funds can be added by web site, phone, mail, or in-person visit. Trips on The RIDE are booked in advance online or by phone, or subsidized on-demand trips can be requested via Uber or Lyft on those companies' mobile apps.

Starting June 22, 2020, the short, urban Fairmount Line was incorporated into the subway fare structure in a pilot program that also started running weekday trips every 45 minutes. In addition to the usual Commuter Rail fare media, CharlieCards are now accepted by tapping at fare vending machines and obtaining proof of payment.

Since the 1980s, the MBTA has offered discounted monthly passes on all modes for the convenience of daily commuters and other frequent riders. As of March 2022, it also offers one-day and seven-day passes (often used by tourists) for subway, bus, inner-harbor ferry, and Commuter Rail Zone 1A. Only the CharlieTicket versions of these passes are accepted on all modes. Single-ride CharlieTickets, weekend passes, 5-ride passes, and the mobile app used for the ferries and commuter rail are not accepted for transfers to buses or subways.

The MBTA has periodically raised fares to match inflation and keep the system financially solvent. A substantial increase effective July 2012 raised public ire including an "Occupy the MBTA" protest. A transportation funding law passed in 2013 limits MBTA fare increases to 7% every two years. Subsequent fare increases took place in 2014, 2016, and 2019.

Several local politicians, including Boston Mayor Michelle Wu, Representative Ayanna Pressley, and Senator Edward J. Markey, have proposed to eliminate MBTA fares.

The remaining phases of the ongoing "Fare Transformation" project aims to add contactless credit cards, Apple Pay, and Google Pay as payment methods for all subway and bus lines so passengers will not need to purchase a CharlieCard or CharlieTicket. It is also expected to add all-door boarding on all buses and surface trolleys, using a proof of payment system. A new website is planned to allow passengers and employers to perform self-service CharlieCard transactions.