As a first-year student in 1897, Allen was the vice president of his class and the captain of the varsity reserve football team.

As a second-year student in 1898, he played at the guard position for the undefeated 1898 Michigan Wolverines football team that won the school's first Western Conference championship.

The season ended with a 5–5 tie in a Thanksgiving Day game with the University of Washington in Seattle.

[11] The 1902 Washington Agricultural yearbook, the Chinook, noted: "The football teams during the season just past have, for the first time in the history of athletics at the W. A. C., had the assistance of a coach.

W. L. Allen, a graduate of the University of Michigan, was procured by the Athletic Association to coach the men; he was very successful and has built a strong foundation for our future in football.