[3][2] In December 1910 joined Woolwich Arsenal (both clubs being owned by the same man, Sir Henry Norris, at the time).
During the 1912–13 season Flanagan finished joint-top league goalscorer (with Charles Lewis) in the First Division.
[4] Flanagan was dropped by Arsenal at the end of 1914–15 and spent the next two seasons as a bit-part player during the First World War.
[4] Flanagan enlisted in the British Army under the Derby Scheme in December 1915, before returning to his reserved occupation as an artillery shell machinist at the Royal Arsenal.
[2] Driver Flanagan died of dysentery at the 52nd (Lowland) Casualty Clearing Station in Mingoyo on 31 August 1917.