The first brownstone cathedral was built in 1854 and named the Cathedral of Saint John and Saint Finbar. It burned in a great fire in December 1861. The rebuilt cathedral was named for St. John the Baptist and was constructed on the foundations of the earlier structure. Architect Patrick Keely designed both the original cathedral and its replacement.
The cornerstone was laid in 1890 by James Cardinal Gibbons of Baltimore, and the church opened in 1907. The spire was not built at the time due to the lack of funds during the construction of the cathedral and its numerous renovations. The church was finally completed on March 25, 2010, with the addition of the steeple and bells.
The cathedral with its new spire is the seventh tallest building in the city.