They were owned by Dan Topping, who transferred the team from the NFL Brooklyn Dodgers, retaining many of the same players.

Former NFL player Jim Barber served as an assistant coach under Flaherty.

The Yankees appeared in the 1946 AAFC championship game, but lost to the Cleveland Browns by a score of 14–9.

The same two teams appeared in the championship game the following year, with the Browns winning again 14–3.

Before the 1949 season, the financially-faltering Brooklyn Dodgers football team was folded and merged into the Yankees, which became the Brooklyn-New York Yankees, but this was the final season of the AAFC, which was then absorbed by the NFL.