Flanagan made his first grade debut for University against Western Suburbs in Round 12 1926 at the Sydney Cricket Ground.
In the grand final, The Students opponents were South Sydney who boasted the likes of George Treweek, Eddie Root and Alf Blair and had gone the previous season undefeated.
A second half fightback by University was not enough and Souths ran out winners 11-5 at the Royal Agricultural Society Grounds in front of 20,000 spectators.
In 1927, University finished last on the table and claimed the wooden spoon in a complete form reversal.
In Flanagan's last season with the club, they finished last on the table winning only 2 games for the entire year.