The contract includes options for two extensions which if exercised could take the total value to $US 4.3bn.
The 14-line 132-station network is the sixth-busiest commuter rail system in the United States, with weekday ridership of around 128,000.
Keolis will take over operations from Massachusetts Bay Commuter Railroad, a Boston-based joint venture between Veolia Transportation, Bombardier, and Alternate Concepts which has run the network since 2003.
Keolis had competed against Veolia Transportation for the contract. "Whoever doesn't get this will be very, very disappointed," Mr Paul Regan executive director of the MBTA Advisory Board, told local media. Regan expressed some concern that the losing bidder might pursue legal action against MBTA due to the high value of the contract. Barring any such action, Keolis is expected to take over operation of the network on July 1.
MBTA General Manager Mrs Beverly Scott said the board concluded that Keolis' proposal represents the best combination of technical quality and price.