The General Synod of the Reformed Presbyterian Church elected Dr. McKinney the first president of Cedarville College in 1894. While president, he continued to serve his congregation in Cincinnati and commuted by train to Cedarville twice weekly to provide leadership in the development of the fledgling institution. Dr. McKinney was known for his energy and determination to see the College well established. He resigned the presidency in June 1915. McKinney Hall, a dormitory constructed in 1999 by Cedarville University, was named in his honor.
