The 1939 Navy Midshipmen football team represented the United States Naval Academy during the 1939 college football season. In their first season under head coach Swede Larson, the Midshipmen compiled a 3–5–1 record and were outscored by their opponents by a combined score of 107 to 88.

Navy was ranked at No. 56 (out of 609 teams) in the final Litkenhous Ratings for 1939.

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