Episcopal City Mission was incorporated in 1844.

In 1846 a wealthy merchant member of St Pauls Church (now St. Pauls Cathedral) made a gift of $50,000 to incorporate the mission and to build a Chapel (the first St. Stevens in Boston) to host the Sunday school and Shelter ministries.

Earlier in the 1900s ECM helped welcome new immigrant groups to Boston with immigrant worshiping communities that gave rise to various parishes.

In 1933 ECM received a bequest of a homestead and $200,000 from Mr. Robert Morville. That bequest has been recycled various times and today it is the new Morville House with 176 apartments for low income elderly in the Fenway.

In 1970 when John Burgess was elected Diocesan Bishop after having been the Superintendent of ECM, the ECM bylaws were changed to include participation of all parishes and missions, focusing its ministry on work for social justice.

With the new structure also came financial independence from the Diocese. Most of ECMs operating budget comes from endowment income; an annual grant for the Burgess Fund is made by the Diocese and the remaining comes from annual appeals and other gifts.