On August 9, 1944, the Presbytery of Philadelphia ordained Gordon Clark.
A complaint against his ordination, filed in the Presbytery and eventually reaching the General Assembly in 1945, launched the "Clark Controversy" within the Orthodox Presbyterian Church. The dispute took place on three levels. First, the complaints noted irregularities that attended the ordination (Clark was licensed to preach and ordained in the same meeting). The General Assembly agreed that the Presbytery erred, but it did not overturn the ordination. Secondly, there were concerns whether Clark's views on divine and human knowledge gave adequate account for the "incomprehensibility of God." Finally, the controversy was part of a larger debate over the direction of the denomination between more Reformed and more evangelical parties.
Convinced that the OPC was becoming too narrow and sectarian, Clark left in 1948, transferring his ministerial credentials into the United Presbyterian Church of North America. Later, he joined the Reformed Presbyterian Church, Evangelical Synod. At the time of his death in 1985, he was retired from teaching philosophy at Butler University and Covenant College.