Newark finished in first place for both halves of the season, so was declared champion. The NNL and the NAL faced each other in the Negro World Series at the end of the season to determine an overall champion.
Champ
NWK
1946 NNL Champion Newark Eagles
z: best record, c: conference winner, y: division winner, w: wildcard, x: clinched playoff spot

Negro World Series

Best of 7-game series
Date    OpponentResultScoreSeries
9/17vs Kansas CityL  1-2 0-1
???vs Kansas CityW  7-4 1-1
???at Kansas CityL  5-15 1-2
???at Kansas CityW  8-1 2-2
???at Kansas CityL  1-5 2-3
???vs Kansas CityW  9-7 3-3
9/29vs Kansas CityW  3-2 4-3