Southeast Missouri State compiled an 8–0–1 record, won the MIAA championship, led the conference in scoring offense and defense, and took six of eleven first-team spots on the 1946 All-MIAA football team.
None of the MIAA teams was ranked in the Associated Press poll or played in a bowl game.
[2][3] Southeast Missouri took six of eleven first-team spots on the Associated Press 1946 All-MIAA football team: backs John Griffith and Webb Halbert; end Roscoe Branch; tackle Kenneth Knox; guard William Sapp; and center Donald Anderson.
In addition, end Jack Klosterman and tackle Bill Lee were chosen for the second team.
In their ninth season under head coach Ryland Milner, the Bearcats compiled a 4–3 record (2–3 against MIAA opponents), finished in fourth place in the MIAA, and outscored opponents by a total of 63 to 57.