From 1892 until 1925, he was professor of Political Economy and director of the School of Economics, Political Science, and History at the University of Wisconsin in Madison. In 1894 an unsuccessful attempt was made by Oliver Elwin Wells, Superintendent of Public Instruction of Wisconsin and "ex officio" member of the University's Board of Regents to expel Ely from his chair at Wisconsin for purportedly teaching socialistic doctrines. This effort failed, with the Wisconsin state Board of Regents issuing a ringing proclamation in favor of academic freedom, acknowledging the necessity for freely "sifting and winnowing" among competing claims of truth.