Born near Castlerea, County Roscommon, O'Flanagan's parents were native Irish speakers. He received his primary education at Cloonboniffe N.S. before traveling to Sligo where he attended secondary school at Summerhill College. He graduated in 1894, and continued his education at St Patrick's College, Maynooth where he was ordained for the Diocese of Elphin in 1900. After joining the priesthood he returned to Summerhill College where he was employed as a teacher until 1904.
O'Flanagan became involved with Irish language revival while teaching. He was a skilled orator and started agitating for radical social and political change. In 1915 was transferred to Cootehall, near Boyle, County Roscommon and was sanctioned by his Bishop when accused of making a speech disloyal to the crown. He also offended nationalists in a letter to Freeman's Journal in June 1916 when he supported Lloyd George's proposal that the twenty-six counties should have immediate home rule.
In late January 1921, during the Irish War of Independence, O'Flanagan met informally in London with Sir Edward Carson and Judge James O'Connor to discuss a peaceful solution to the conflict, but without success. Nearly a year later the Anglo-Irish Treaty was ratified by both sides.
In 1927 he was suspended from clerical duties because of his nationalist activities.
In March 1926, Sinn Féin held its Ard Fheis. Flanagan and Mary MacSwiney led the section from which Éamon de Valera broke away. The conference instructed a joint committee of representatives from De Valera's faction and that of Flanagan to arrange a basis for co-operation. The Ard Fheis issued a statement declaring "the division within our ranks is a division of Republicans."  The split concerned entry to Dáil Éireann in 1926. De Valera took the great majority of Sinn Féin support with him when he founded Fianna Fáil but O'Flanagan maintained his radical stance on social issues in the republican journal An Phoblacht.
-  O'Flanagan at Sligo Heritage. Retrieved 16 October 2007.
- Patrick Murray, ‘O'Flanagan, Michael (1876–1942)’, Oxford Dictionary of National Biography, Oxford University Press, 2004
- No. 129 UCDA P150/1902 http://www.difp.ie/docs/volume/1/1921/129.htm
- The Times, Irish Republican Split. Search For Basis Of Cooperation 13 March 1926
- Patrick Murray, "O'Flanagan, Michael (1876–1942)", Oxford Dictionary of National Biography, Oxford University Press, 2004
- Cronin, Seán (1981). Irish nationalism: a history of its roots and ideology. Continuum. p. 279. ISBN 9780826400628.
|Party political offices|
Jennie Wyse Power (1911–)
|Vice-President of Sinn Féin
with Arthur Griffith (1917–1922)
P. J. Ruttledge
|Leader of Sinn Féin
Cathal Ó Murchadha