The original St. Paul's Church building, a former meeting house of the Shepherd Congregational Society on the site of what is now Harvard University's Holyoke Center, was purchased by Fr.

The cornerstone for the present church building, an Italian Romanesque monument located at Quincy Square (corner of Bow and Arrow Streets), was laid in November 1916 under the leadership of then-pastor Rev.

The architect was Edward T. P. Graham, a St. Paul's parishioner, graduate of Harvard University, and winner of the first Traveling Fellowship to Rome and the École des Beaux-Arts.

An organ of 35 stops was built for the original church building in 1904 by Jesse Woodberry & Co (Opus 251), designed by Edward MacGoldrick.

In 2015 plans were finalized to return the console to its original position in the organ gallery, and the digital voices were all removed, along with the neo-baroque pipework.