In 1989, Flanagan joined the Western Suburbs Magpies. In his second game for them, he accused his Brisbane Broncos opponent Andrew Gee of biting, showing the referee a mark on his forearm. The Magpies’ CEO later decided not to take any action against Gee. In round 8, Flanagan scored his first top-grade try in a tight victory over St. George at Kogarah Oval. He scored his second and final try of the year in round 16, darting over from dummy-half.
