[2] A ruckman, after a single game for Collingwood in the VFA in 1896, the Benalla-born Flynn started his career in earnest in 1897 where he was part of Geelong's inaugural VFL side.

He was made Carlton captain in 1905, and in 1906 led them to the premiership, defeating Fitzroy in the Grand Final.

Due to business commitments in St James, running the local hotel (pub) which still operates today (37 kilometres north of Benalla), he retired from football; however, he returned for the 1907 finals series after captain Fred Elliott was suspended.

[citation needed] In 1908, Flynn did not play a game during the home-and-away season but was again used by Carlton in the finals, this time under the captaincy of Elliott, and was a member of a premiership side for the third successive year.

[5] Flynn is buried at Lake Rowan, east of St James, Victoria, beside his wife and 10-year-old daughter Annastasia.