Stuart leaving the club ended yet another tenure prematurely and at loggerheads with club executives, members and players, with Cronulla appointing Shane Flanagan as his replacement. Stuart signed a lucrative three-year contract with the Parramatta Eels, beginning in 2013. This meant that Stuart had to stand down as the head coach of the New South Wales State of Origin team, as the state had put in a policy that the head coach would not have any relation to an NRL club. The Eels had in recent years been perennial underachievers, with Stuart set the unenviable task of resurrecting the team after the team finished last in 2012. However, in the round 4 match against the Roosters, Stuart suffered the worst defeat in his NRL coaching career, losing 50-0. In the aftermath of the game, Stuart said at the press conference "I can't say it won't happen again, it will and I hope to turn it around quickly but it won't, it is going to take a long time to turn it around, we have to keep building our roster because it is not up to the level of other rosters". In April 2013 Stuart was fined $10,000 for questioning a referee's impartiality following a loss to the Gold Coast. On 11 September 2013, Stuart announced that he was quitting the Parramatta Eels to join the Canberra Raiders as head coach on a three-year contract to continue his coaching career. Stuart took up the head coach position of the Canberra Raiders on a three-year deal in 2014. Following Canberra's loss in round 10 of the 2014 NRL season, Stuart spoke to the media saying "When you get shit refereeing, sorry, when you get poor refereeing decisions that are just incorrect, purely incorrect, that frustrates you because it’s a tight competition and every game’s a tight game". Stuart was later fined $10,000 by the NRL for his post match comments. In 2016, Stuart coached Canberra to a second-placed finish at the end of the regular season. In week one of the finals, Canberra were upset in front of a sold-out home crowd losing to eventual premiers Cronulla 16-14. Canberra would go on to defeat Penrith the following week to qualify for the club's first preliminary final in 19 years. Canberra went on to fall short of a grand final appearance losing to Melbourne 14-12. In July 2018 after a match against the Cronulla-Sutherland Sharks in which a refereeing mistake led to a try lost the raiders the game, Stuart demanded that the NRL overhaul the bunker system responsible to reviewing potential tries.