Howe enrolled at Yale University in 1908. He played for the Yale Bulldogs football team as a quarterback from 1909 to 1911. As a sophomore in 1909, Howe led the team to a perfect 10–0 record, as the Yale team outscored its opponents by a combined score of 209–0. At the end of the 1909 season, Howe was selected as a second-team All-American by Walter Camp. After another strong year in 1910, Howe was unanimously elected by his teammates as the captain of Yale's 1911 football team. As a senior, he set a collegiate record by returning 18 kicks in a November 1911 game against Princeton. After the 1911 season, Howe was selected as the first-team All-American quarterback by "Collier's Weekly" (as selected by Walter Camp), "The New York Globe", W.S. Farnsworth, Dr. Henry L. Williams, and Charles Chadwick.