Agase remained as an assistant until Parseghian left to coach at Notre Dame in 1963 and he was named the new head coach. Agase guided the Northwestern Wildcats to a 32–58–1 win-loss-tie record in nine seasons. He was named coach of the year by the Football Writers Association of America after guiding the team to a 6–4 record in 1970. Agase left to coach at Purdue in 1972, but none of his teams posted a winning record there, and he was fired in 1977. He then spent six years as athletic director at Eastern Michigan University before retiring. Agase died in 2007. He was inducted into the College Football Hall of Fame in 1963.