Saint Paulus Lutheran Church was founded on May 15, 1867, by 23-year-old Pastor Jacob Buehler — a man whose conviction and drive would earn him the title "Father of Lutheranism on the Pacific Coast." He had come to San Francisco to help establish St. Mark's Lutheran Church in 1860, but theological conflict forced his resignation just a few years later. Buehler and a small following immediately founded Saint Paulus, which would become the most prominent Missouri Lutheran Synod churches on the West Coast.

The congregation grew rapidly, moving twice in two years before settling on Mission Street for the next quarter century. By its 25th anniversary, membership had reached 1,400 souls. In 1872, Saint Paulus founded the first Lutheran day school west of the Rocky Mountains. Missionary pastors were sent out, planting congregations across the Bay Area and Central Valley.

By 1894, a towering new church rose at Eddy and Gough – just two blocks from St. Mark's – three spires, reaching 175 feet into the San Francisco sky, costing $65,000 and announcing a church that intended to stay.