There was no championship game in 1939.
In a meeting of the owners of the APFA on January 7, 1940, the Columbus Bullies were announced as league champions.
In a meeting of the owners of the APFA on January 7, 1940, the Columbus Bullies were announced as league champions.
| Team | W | L | T | Pct | ||
 | Los Angeles Bulldogs | 7 | 1 | 0 | .875 | |
| | Cincinnati Bengals | 6 | 2 | 0 | .750 | |
| | Columbus Bullies | 9 | 4 | 0 | .692 | |
| | Chicago Indians | 4 | 3 | 0 | .571 | |
| | St. Louis Gunners | 5 | 6 | 0 | .455 | |
| | Dayton Bombers | 2 | 5 | 0 | .286 | |
| | Kenosha Cardinals | 2 | 7 | 0 | .222 | |
| | Louisville Tanks | 2 | 9 | 0 | .182 |