John Lynch was born in the United Kingdom and moved to his father's native home in Corrinshego, County Armagh, near Newry in Northern Ireland as a child. He attended St Colman's College, Newry, a Catholic school. He began acting in Irish Language plays at school during the early years of the conflict in Northern Ireland. He is the eldest of five children. He has said his family were "affected" by The Troubles but like everyone else they got on with our lives. His mother is Italian and his father is Irish. He is also a novelist. His first novel, Torn Water, was published in November 2005 by the Fourth Estate, a literary imprint of Harper and Collins, and his second, Falling Out of Heaven, was published on 13 May 2010 by the same publisher. He separated from Mary McGuckian, in 2008 and the marriage was annulled mid-2012.
Lynch played the part of football legend George Best in the 2000 film Best. He also played the lead in the Australian feature Angel Baby, winning the Australian Film Institute award for best leading actor and the Australian Film Critics award for best actor of 1995. He was nominated for a Satellite Film Award for the film Moll Flanders in 1996. He worked with acclaimed Belgian director Marion Hansel on her adaptation of Booker-nominated author Damon Galgut's novel The Quarry, which won Best Film at the Montreal Film Festival. He won Best Actor for the lead role in Best at the Fort Lauderdale Film Festival in 2000. He wrote and co-produced the film. He was nominated for a BAFTA for the film Cal. He has also been nominated for an Irish Film and Television Award for his role in the ITV film The Baby War. He has also starred in the film Five Day Shelter playing the role of Stephen, which won a European Film Award and was in competition at the Rome Film Festival. More recently, he has played the lead in Craig Vivieros' first feature film, the prison drama Ghosted. He played the role of Wollfstan in Christopher Smith's film The Black Death, and also played a sergeant major in Pat O'Connor's well received film of the Michael Morpurgo novel Private Peaceful.