Farrell was born in Dublin, the son of Rita, a housewife, and Eamon Farrell, a footballer who played for Shamrock Rovers FC (Rovers) and owned a company importing and exporting canned goods in Dublin City. He was raised Roman Catholic. His uncle Tommy Farrell also played for Rovers. Farrell has two sisters, Claudine (who is his personal assistant) and Catherine, and a brother, Eamon Jr. When he was ten, the Farrells moved to Castleknock, a Dublin suburb. Farrell was educated at St. Brigid's National School Castleknock followed by Castleknock College and Gormanston College. Farrell auditioned for the Irish group Boyzone when he was still unknown, but was unsuccessful. Farrell attended The Gaiety School of Acting, but dropped out and was cast in the part of Danny Byrne on Ballykissangel, a BBC television drama. Farrell appeared on the show 7 times from 1998 to 1999.
Farrell has mentioned in interviews that he is uncircumcised, and also that he is against circumcision. Farrell was married to English actress Amelia Warner from July 2001 to November 2001. Farrell has a son, James Padraig (born 12 September 2003), with US model Kim Bordenave. In October 2007, Farrell revealed that his son has Angelman Syndrome, a rare genetic disorder characterized by intellectual and developmental delay, speech impediment, sleep disturbance, seizures, hand flapping movements, and frequent laughter/smiling.
In December 2005, Farrell voluntarily checked into a rehabilitation treatment center for addictions to recreational drugs and painkillers His publicist commented that Farrell had started taking painkillers due to a back injury. He was released in January 2006. In May 2006, Farrell started attending rehabilitation meetings.
It was announced on 14 September 2009, that Farrell and his Ondine co-star Alicja Bachleda-Curus were expecting a child together. Their son, Henry Tadeusz Farrell, was born on 7 October 2009 and was baptised in the Catholic Church of the Visitation of the Blessed Virgin Mary, Krakow, Poland.
It was reported on 15 October 2010 that the couple had split up.