[2] St. Stephen's Church was founded in 1867 as the first organized Protestant congregation in San Luis Obispo County by local physician Dr. William Hays.

[3] The church was completed in October 1873,[5] built in the Carpenter Gothic architectural style, and was consecrated by Bishop of California William Ingraham Kip.

[3] Upon its completion, St. Stephen's was erroneously described as a Methodist church in an article by the San Luis Obispo Tribune.

In the 1950s the rectory was demolished and replaced with an education building containing classrooms, offices, a library, and meeting rooms.

[1] The church was repaired with the assistance of architect John Stuart and the Bunnell Construction Company.