The present church was built in 1859.  Lay readers conducted the early services, among them Captain Julian McAllister.  In 1976 St. Paul's became the first Episcopal Cathedral for Northern California with the Reverend J.H.D. Wingfield as bishop.

Work on the building was done by Scandinavian shipwrights from the Pacific Mail and Steamship Company.  The nautical heritage is reflected in the ceiling, which resembles an inverted ship's hull and is similar in design to the Norwegian Staves Churches.  California redwood with wooden dowels were used in this edifice, which has a floor plan shaped like a cross.