California's first Archbishop, Joseph S. Alemany, laid the cornerstone July 21, 1861. The first mass was celebrated Christmas Eve of the same year.

In 1870 the transept was added. The present steeple and ornate façade date from 1893.

Saint Mary's is the oldest Catholic parish in the San Joaquin Valley.

St. Mary's Catholic Church was designated as Stockton Historic Landmark No. 1 in 1971.