The parishioners of Saint Paul’s held their first service in a room over a lower Union Street stable on Christmas Day, 1849. In 1850, the congregation constructed and moved to the first Saint Paul’s Church on Carroll Street between Hicks and Henry Streets.

In the wake of the Civil War, spurring Brooklyn’s industries, Saint Paul’s continued to thrive and expand. In the spring of 1866 the vestry purchased land at the corner of Clinton and Carroll Streets and commissioned Richard M. Upjohn, a member of the vestry and one of the nation’s most prominent Gothic Revival architects, to design the granite and limestone building that stands today. The congregation celebrated its first service here on September 19, 1869, though the church wasn’t consecrated until 1884, when the building loans were paid in full.