The church was established in 1958 as a part of the Presbyterian Church USA denomination (PC(USA) for short).
A Denominational Task Force was appointed in January of 2012 to study the theological crisis taking place in the Presbyterian Church (USA). This task force met for nearly twenty months to study, share, pray, and discern what the future looked like for St. Luke JOY and the PCUSA. Ultimately the task force recommended moving from the PCUSA to the Evangelical Presbyterian Church, and the session unanimously agreed. A congregational meeting was held in November of 2013 where 96% of those in attendance voted to disaffiliate from the PC(USA) and affiliate with the Evangelical Presbyterian Church. St. Luke JOY formally joined the Evangelical Presbyterian Church in April of 2014.