Purcell's three brothers and one sister live in Dundalk and hold Irish citizenship. In August 1997, Purcell started dating Rebecca Williamson. They married on 1 August 1998 after one year of dating and have four children together: son Joseph (born 12 August 1999), daughter Audrey (born 30 January 2001) and twins Lily-Rose and Augustus (born 7 July 2003). In October 2007, Purcell and Williamson separated, and divorced on 22 October 2008. Since 2011 he is dating former 90210 star AnnaLynne McCord the couple announced an amicable split in 2014 but rekindled their romance a year later, McCord told People Magazine she came back into his life as friend when the actor was diagnosed with skin cancer but soon became romantic again.
On June 1, 2016, Purcell suffered severe injuries on set in Morocco, after a misplaced iron bar used as a Prison Break (new miniseries) set piece had fallen onto his head. The Australian actor was immediately airlifted from Marrakesh to Casablanca, where he received emergency treatment for nasal fractures and various other injuries. As of June 7, Purcell is recovering, and the filming schedule has been adjusted to minimise disruption.