The 1939 NCAA Cross Country Championships were the second annual cross country meet to determine the team and individual national champions of men's collegiate cross country running in the United States. Since the current multi-division format for NCAA championship did not begin until 1973, all NCAA members were eligible. In total, 19 teams and 67 individual runners contested this championship. The team national championship was won by the Michigan State Spartans, their first, while the individual championship was won by Walter Mehl from Wisconsin, with a time of 20:30.9.