He joined the Ulster Rugby academy for the 2008–09 season.[6] He signed a development contract ahead of the 2010–11 season, and made his debut for the senior team against Ospreys in September 2010[5] He made 15 appearances, including eight starts, in the Pro12 that season, as well as four appearances off the bench in the Heineken Cup. The following season he made 16 appearances, including eight starts, in the Pro12, and five appearances, including one start, in the Heieneken Cup.[7] He was named in the Ireland squad for the 2012 Six Nations Championship, but was unable to play because of a minor knee injury.[8]
In August 2012 he sustained a serious knee injury while training in France,[9] and two months later his close friend and teammate Nevin Spence died, leading to a period of depression.[8] In the summer of 2014 he moved to Aurillac in the French second division, then coached by former Ulster player Jeremy Davidson.[10] The following season he was signed by another former Ulster player, David Humphreys, to play for Gloucester in the English Premiership.[11] After four season with Gloucester, he returned to Ireland with Connacht.[12]
In August 2020, his wife Deborah suffered a stroke while pregnant with their third child. She made a full recovery and the child was born healthy, but McAllister decided that "family had to come first",[13] and announced his retirement at the end of the 2020–21 season.[14] After retiring as a professional player, he took a job as head of commercial and income revenue for All-Ireland League club Belfast Harlequins, while also playing and coaching for the club.[13] Paddy moved to Banbridge RFC in 2023 to take up the role as assistant coach.