[4] While at college at the University of Pittsburgh, Milligan played guard from 1929 to 1931 under the school's legendary coach Jock Sutherland.

The 1929 Pitt team went undefeated in the regular season and won the Eastern Championship[6] and appeared in the Rose Bowl losing to USC.

The loss did not prevent football historian Parke H. Davis from naming Pitt as that season's national champion.

Milligan brought Pitt back to winning records in 1948 and 1949, achieving consecutive 6–3 seasons that included appearances in the national rankings and back-to-back shutouts of Penn State, the first of which snapped Penn State's 17-game unbeaten streak.

After Pitt, a twenty-point underdog,[14] defeated defending Rose Bowl champion Northwestern on the road on October 1, 1949, Milligan was named the United Press "Coach of the Week".

[1] However, Milligan resigned on January 27, 1950,[15] due to a perceived snub by the university offering him only a one-year contract, and he never returned to a head coaching position.