The Blue Line is Boston's second-oldest subway. The oldest part is the East Boston Tunnel, which crosses underneath Boston harbor from Maverick to what is now Government Center. When it was opened at the end of 1904, it allowed trolleys to run from East Boston to a stub terminal at Court Street Station, located next to Scollay Square Station (now Gov't Center). This was extended to the current terminus at Bowdoin in 1916 (the floor of Court Street was dropped down to make the current Blue Line platform at Gov't Center). At Bowdoin there was a portal onto Cambridge Street and a trolley loop (the latter is still in service). In 1924 the tunnel was converted to third rail operation. The subway cars used the existing surface tracks on Cambridge Street and across the Longfellow Bridge to access the Red Line's now-gone Eliot Square Shops via a connecting switch on the Cambridge end of the bridge.

In 1952 the Revere Extension opened as far as Orient Heights, using the grade of the abandoned narrow-gauge Boston, Revere Beach & Lynn RR. With the simultaneous opening of the Blue Line's shops at Orient Heights, the portal at Bowdoin and the connection to the Red Line were abandoned (ironically, there are plans to rebuild most of this connection). The rest of the extension to Wonderland opened in 1954. Oddly, the surface parts of the Blue Line (Airport to Wonderland) use catenary instead of third rail for power.

Most service on the Blue Line is now provided by a fleet of 94 #5 East Boston Tunnel cars in the 0700 series, built by Siemens.  0704 and 0705 were the first to be delivered, and were originally based at the Orange Line's Wellington Shops, where they had access to the otherwise unused third track between there and Community College (now dubbed the "test track").  The first cars of this fleet, 0708-0711, entered service on February 20, 2008.  Twenty-two #4 EBT cars (in the 0600 series) built by Hawker-Siddeley in 1978-80 are still around, but they are used only in rush hour service.  Strangely, the T refuses to run them in 6-car trains.  The 0600s are known as Bluebelles, and are largely identical to the #12 cars on the Orange Line.