Air Force removed its leading rusher in 2018 from the team.
"Cole Fagan has been removed from the team pending an ongoing investigation," the Air Force Academy said in a statement.
Fagan's profile page has been taken off the Falcons' football website.
As a junior in 2018, Fagan rushed for 997 yards and seven touchdowns in 12 games.
Troy Garnhart, Air Force's associate athletic director for communications, told The Gazette in Colorado Springs that Fagan was taken off the team in April but would not elaborate on the school-issued statement.
Fagan, from Dunnellon, Fla., is the son of former NFL defensive end Kevin Fagan, who played for the San Francisco 49ers from 1987-93.
Air Force finished with a 5-7 record last season. The Falcons open the 2019 season on Aug. 31 against Colgate.