Born and raised in Ballinamore, County Leitrim, McGirl became involved with the Irish Republican Army in the 1930s. He was arrested along with Cathal Goulding and ten others in 1946, and sentenced to 12 months in prison for IRA membership. McGirl participated in the IRA Border Campaign. In January 1957, he was tried and convicted at Ballinamore courthouse and imprisoned in Mountjoy Prison. Although a prisoner, he was elected as a Sinn Féin Teachta Dála for the Sligo–Leitrim constituency at the 1957 general election, topping the poll with 7,007 votes. Running on an abstentionistticket, Sinn Féin won four seats at the general election. McGirl did not retain his seat at the 1961 general election. His share of the vote was halved and he received only 2,487 votes. In November 1957, he delivered the oration at the funerals of some of the "Edentubber martyrs", four IRA members who were killed when a bomb they were preparing accidentally exploded. In 1962, he served on the committee that founded St. Felim's College, Ballinamore.
Provisionals
When the IRA split in 1969, between "Official IRA" and "Provisional IRA" factions, McGirl sided with the Provisionals, who were committed to launching an armed campaign against British rule in Northern Ireland. He was interned in Northern Ireland in 1974. McGirl contested the February 1982 and 1987 general elections in the Republic. In the former contest, he received 2,772 votes and in the latter, 2,627 votes. McGirl served as vice-president of Sinn Féin. Originally he was opposed to the dropping of the Éire Nua policy and was considered an ally of Ruairí Ó Brádaigh. However, at the 1986 Sinn Féin Ardfheis, McGirl supported the moves of Gerry Adams and Martin McGuinness to drop the policy of abstentionism, greatly angering his contemporaries Ó Brádaigh and Dáithí Ó Conaill. McGirl was a publican, undertaker and bicycle-repairer in Ballinamore. He was first elected a Sinn Féin councillor to Leitrim County Council in 1960, serving as chairperson of that body. He was still a member of the council at the time of his death. After his death, a monument was erected to McGirl in his native town of Ballinamore. It is located on the bridge crossing the Shannon–Erne Waterway. A nephew, Francis McGirl, was charged but acquitted of the murder of Lord Mountbatten, who was killed by the IRA when his boat was bombed off the Sligo coast in 1979. John Joe's son, Liam McGirl, was co-opted on to Leitrim County Council in 1988 after his father's death. He was subsequently re-elected until 2001, when he retired and handed the seat over to Martin Kenny.