McGovern switched from Wesleyan Methodism to less fundamentalist regular Methodism. Influenced by Walter Rauschenbusch and the Social Gospel movement, McGovern began divinity studies at Garrett Theological Seminary in Evanston, Illinois, near Chicago. He preached as a Methodist student supply minister at Diamond Lake Church in Mundelein, Illinois, during 1946 and 1947, but became dissatisfied by the minutiae of his pastoral duties. In late 1947 McGovern left the ministry and enrolled in graduate studies at Northwestern University in Evanston, where he also worked as a teaching assistant. The relatively small history program there was among the best in the country and McGovern took courses given by noted academics Ray Allen Billington, Richard W. Leopold, and L. S. Stavrianos. He received an M.A. in history in 1949.