Huarte played college football for the Notre Dame Fighting Irish. During his sophomore and junior seasons, he averaged only a few minutes per game due to injuries and the Irish went 5–5 and 2–7, respectively. As a senior, however, he became the starting quarterback as the Irish won all but one game during the 1964 season, in which he was selected as an All-American and won the Heisman Trophy. By the end of the season, Huarte threw for 2,062 yards with only 205 passes, an average of over ten yards per pass attempt, many to receiver Jack Snow.