Flanigan was drafted by the Green Bay Packers[2] in the 2nd round (51st overall) of the 1967 NFL/AFL draft. He played 40 games for the Packers between 1967 and 1970. He was a member of the Super Bowl Champions of 1967. He also played at middle linebacker in 14 games for the New Orleans Saints in 1971, giving him a total of 54 professional games.