In autumn 1903 he became a student at St. Patrick's College, Maynooth, again achieving great distinction in subjects such as Irish, French, Italian and Philosophy.
Tomás Ó Fiaich later commented that Walsh was one of "... a generation of students [at Maynooth] which was collectively able, multi-talented, committed and independent-minded", many of whom went on to achieve great distinction in many aspects of Irish life.
However, his participation in a controversy concerning 'compulsory Irish' at the National University led to him been denied ordination at Maynooth; the ceremony instead took place at All Hallows College, Dublin, on 24 June 1909.
In April 1916 he was a minor participant in the run-up to the Easter Rising, when he became a member of the various groups sent by Eoin MacNeill to countermand Sunday 'manoeuvres, travelling as far as Athenry, County Galway.
Due to his shy nature he was reputed to be a poor lecturer and was thus relieved to be appointed curate of Eglish, Birr, County Offaly.
His health declined precipitously in spring 1941, and following a brain haemorrhage, Walsh died at the Pembroke Nursing Home, Dublin, on 18 June 1941.
In 1915, Walsh produced part one of The Placenames of Westmeath, and abridged version of John O'Donovan's 1837 Ordnance Survey letters for the county.
Paul Walsh's first work concerning Ulster was his edition of the diary of Tadhg Ó Cianáin, which was a journal of the Flight of the Earls.
However, this led to a "series of meticulous and penetrating studies that were to shed a great deal of light on the story of Mícheál Ó Cléirigh and the Four Masters" (#4), all of which were published in the 1930s and are still invaluable.