Farrell married English actress Amelia Warner in July 2001 and divorced her four months later.

Farrell has a son, James (born September 12, 2003), with American model Kim Bordenave, from whom he has since separated. In October 2007, Farrell revealed that his son has Angelman Syndrome, a rare genetic disorder characterised by intellectual and developmental delay, speech impediment, sleep disturbance, seizures, hand flapping movements, frequent laughter/smiling and usually a happy demeanour.

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.

He currently owns property near Phoenix Park in Dublin, but is living in a home he owns in Los Angeles to be near his son, James, who turned four in 2007.