In April 2010, Flanagan was appointed after Brendan Hackett resigned due to a disastrous league campaign with the team being relegated to Division 3.
[4][5][6] He was then given unanimous support to continue; though Flanagan asked for a two-year term, this was not granted as county bye-laws had it that the manager must be ratified every year.
[7] The year 2011 proved to be a great improvement as Weatmeath qualified all the way to promotion to Division 3 where the faced Leinster finalists Louth.
2013 proved to be the best success as The Lake County gained promotion to Division 1 for the first time since 2008 despite narrowly losing to opponents Derry.
Flanagan's team were then throttled by Dublin in the Championship, prompting the manager to express concern about the ever increasing gulf opening up between counties.
[18][19][20] After Davy Burke was appointed to the Roscommon managerial vacancy, Flanagan quit as Pearses manager in November 2022, after five seasons.