The Orange Line has a long and interesting history. It was originally called the Main Line Elevated, and between when it was built and the present virtually the entire line has been realigned.

When the Main Line El was originally opened in 1901, it had two branches between North Station and what is now Back Bay. The Main Line went through the Tremont Street Subway on the two outer tracks (which are continuous through the subway's entire length, while a branch ran on the Atlantic Avenue Elevated. In 1908, the Main Line was relocated from the Tremont Street Subway into the current Washington Street Subway. The Atlantic Avenue El was abandoned in 1938 and torn down in 1942 as part of Boston's contribution to the war effort. In 1975 the Charlestown Elevated was replaced by the Haymarket North Extension to Sullivan Square, which used a tunnel under the Charles River. From just south of Community College to Oak Grove (reached in 1977), the line uses an old Boston & Maine RR right of way. Finally, in 1987 the Washington Street Elevated was replaced by the Southwest Rail Corridor. Only the 1975-7 extension to Oak Grove is on its original right of way now.

The cars on the Orange Line, which are in the 01200- and 01300-series, are known as "Orange Blossoms". They were built in 1979-81 by Hawker Siddeley and are virtually identical (though larger) to the Blue Line's now-retired #4 East Boston Tunnel cars.