After earning his doctoral degree, Fetter accepted an instructorship at Cornell, but quickly left after being offered a position as a professor at Indiana University. In 1898, Stanford University lured him away from Indiana, but Fetter resigned from Stanford three years later over a dispute regarding academic freedom. After leaving Stanford in 1901, Fetter went back to Cornell, where he remained for ten years. In 1911, he again found himself in professional transition, accepting the position of chairman in an interdisciplinary department at Princeton University which incorporated history, politics, and economics. Fetter was the first chairman of Princeton University's Department of Economics and Social institutions.