The 1946 Allen Yellow Jackets football team was an American football team that represented Allen University of Columbia, South Carolina, in the Southeastern Athletic Conference (SEAC) during the 1946 college football season. William "Buster" Lawson and Hooks Nelson were the team's coaches. The team compiled an overall record of 8–2 with a mark of 5–0 in conference play, winning the SEAC title. The Yellow Jackets lost the first two games of the season and then won the remain eight games, including a victory over Fayetteville State in the Piedmont Tobacco Bowl.
The Dickinson System rated Allen as the No. 11 black college football team for 1946.
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