The Yaphank Presbyterian Church had its beginnings according to church and county records in the late 1700s. In 1817 the local Millville (Yaphank) schoolhouse on Sundays hosted a Sunday School mission of the Middle Island Presbyterian Church. After a number of years of worshipping in homes and in the schoolhouse, the present church was built as a chapel in 1851. In October 1871 the Yaphank Presbyterian Church was officially recognized as an individual church by the Long Island Presbytery.
Over the years the church has been a center of community activities for Greater Yaphank. Community organizations presently using the church facilities include various after school programs, scouting groups, Alcoholics Anonymous, the Yaphank Cemetery Association, The Yaphank Summer Day Camp, Totally Kids Pre-School Nursery, Suffolk United Veterans and the Food Closet of the Board of Deacons. The first stage of a Community Services Building was erected in 1997 with the help of both church and community volunteers. The second phase which includes toilet and kitchen facilities was added in 2003. A third phase to include a multi purpose room for banquets, meetings and recreations is presently being planned. Yaphank Presbyterian is one of seven member churches of the Mid-Suffolk Parish of the Presbyterian Church.