Organized in 1861, the congregation built its first church building on the southwestern corner of the intersection of Washington and Webster Streets, two blocks away from the Henry County Courthouse.

Approximately forty years later, the original building was destroyed and the present structure erected on its place; construction began in 1900 and concluded in 1901.

[2] Unlike those of many sandstone buildings, the walls of First Presbyterian are built of stones of many different sizes and colors.

[2] Its unusual shapes and colors present a significant contrast to St. Augustine's Catholic Church, located on the other side of downtown Napoleon:[1] while First Presbyterian includes a broken roofline and the many decorative elements typical of the American Craftsman style, St. Augustine's is a uniform Gothic Revival structure with a tower 200 feet (61 m) high.

When the presbytery last compiled statistics, the congregation reported 133 members; at that time, it was served by Pastor Gavin Pitt.