On February 23, 1849, the Rev. John W. Douglas, a young Presbyterian minister, arrived at Monterey Bay, California via steamship. In March 1849, he began his ministry in San Jose, California. The church, which was called "Independent Presbyterian Church," first met in the "Juzgado," a building which at the time also served as both a courthouse and as a jail (see San Jose City Hall).
In 1851, a wooden church was built on North Second Street, across the street from the present Trinity Episcopal Cathedral.
On June 3, 1858, the church changed its name to "First Presbyterian Church," and has been called that ever since.
In just over a decade, the original wooden building was considered to be too small. A new brick church building was built in 1863. This building was repaired after the earthquake of 1868, and was in use until the 1906 San Francisco earthquake demolished that church building.
A new church building, located at 48 N. 3rd Street, was completed and dedicated in April 1908. That building was in use for several decades, until 1968, when it was condemned as a fire hazard.
A new and smaller church building was built on 49 N. 4th Street, and has been in use since 1973.
On June 30, 2019, the First Presbyterian Church of San Jose held its last Sunday service, which was attended by members, friends and guest musicians. The congregation voted to dissolve, due to declining membership. The programs that benefit people who are homeless will continue for now.