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".