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 meet was hosted by Michigan State College at the Forest Akers East Golf Course in East Lansing, Michigan for the second consecutive time. Additionally, the distance for the race was 4 miles (6.4 kilometers).

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.

Men's title Distance: 4 miles Team result Rank Team Points Michigan State 51 Wisconsin 57 Indiana 84 Drake 104 Oklahoma A&M 114 Michigan State Normal 129 Alfred 138 Notre Dame 217 Ohio State 227

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