In 1886 several Episcopalian families met in the Guild Hall at Bryn Mawr and Winthrop Avenues (the first commercial building in the Edgewater neighborhood then on the outskirts of Chicago), and decided that a Church should be built.

By June 17, 1888, then-lawyer Frederick W. Keator held a service in the hall, and by November 1888 the group had become a mission congregation within the diocese, taking as the name of Church of the Atonement.

The original Church's cornerstone was laid on November 30, 1889 at the present site (the intersection of Kenmore and Ardmore Avenues), and consecrated in June 1890.

Stained glass windows were added beginning in 1929, under Rector Alfred Newberry (1927-1937; who would ultimately leave to accept a call from the Church of the Advent in Boston) and finished in 1946.

Under Rector Dean Paxton Rice, the church received a donation of an Elizabethan-era paneled room (installed in the Parish House), and also expanded its outreach to the diverse and changing neighborhood.

Parishioner Henry Ives Cobb designed the original church building, including a stone tower on the northwest corner and constructing the east wall of wood to facilitate future expansion.

Cobb was known for his English Gothic and Richardson Romanesque buildings, including the Potter Palmer Mansion, the Newberry Library and the Old Chicago Historical Society on Dearborn and Ontario Streets (now a nightclub).