Flynn joined the Dublin senior team in 1957. He took over from Paddy O'Flaherty as first-choice goalkeeper following his retirement in September 1959. Flynn won back-to-back Leinster Championship medals in 1962 and 1963, and was on the Dublin team that defeated Galway to win the 1963 All-Ireland Senior Football Championship final.[1][2] Flynn ended his career with a third provincial winners' medal in 1965.