Named after local missionary to the Indians, John Eliot, the square was the site of the Roxbury town center after its founding in 1630.

John Eliot Square's central landmark is the First Church of Roxbury, Boston's oldest surviving wooden meeting house from the Federal Period of American architecture.

[7] While Thomas owned the house in 1776, cannons from Fort Ticonderoga in New York were transported by Henry Knox to Cambridge, Massachusetts and then through Roxbury on the way to forming the Fortification of Dorchester Heights, where they were used to force the evacuation of the British from Boston on March 17.

[8] A marker commemorating the neighborhood as a stop on the Knox trail and signifying Thomas' role in ending the Siege of Boston was placed at the park in 2009.

[5] After two fires in the 1970s, a state representative who was a former Roxbury resident successfully petitioned the legislature in 1984 for funding to restore the house and preserve it as a heritage park.