In Round 12, Mortimer made his NRL debut for the Eels against the Cronulla-Sutherland Sharks at five-eighth in the Eels 13–10 loss at Parramatta Stadium. In Round 16 against the Brisbane Broncos, Mortimer scored his first NRL career try in the Eels 21–14 win at Parramatta Stadium. Mortimer went on to score 10 tries from 18 games in his rookie season, helping the Eels to make it to the 2009 NRL Grand Final in a late season surge, playing at five-eighth against the Melbourne Storm in the Eels 23–16 loss. In 2018, Mortimer recalled his memories of the 2009 grand final saying "It was a whirlwind, it was surreal. It feels like a movie I watched. I don't think we've seen a team do that since, to be so far out of the eight then to go on to the grand final, it was an absolute buzz, something I'm so thankful I was a part of it".
2010
In 2010, after a lacklustre start to the season, Mortimer reflected on 2009 saying, "We hit form that not many teams have done in the history of footy, so to be judged on that's pretty harsh". Mortimer finished the 2010 NRL season with him playing in 21 matches and scoring 2 tries for the Parramatta Eels. During the 2010 season, Mortimer was reportedly offered $500,000 a season to join rivals Canterbury where is father Peter Mortimer played but turned down the offer to remain at Parramatta until the end of the 2012 season.
On 7 May 2013, Mortimer re-signed with the Roosters on a 2-year contract. On 6 October 2013, Mortimer played in the Sydney Roosters 2013 NRL Grand Final team against the Manly-Warringah Sea Eagles off the interchange bench in the Roosters Grand Final 26–18 win. Mortimer finished the 2013 NRL season with him playing in all of the Roosters 27 matches, scoring 5 tries and kicking 2 goals.
2014
On 22 February 2014, Mortimer played in the Sydney Roosters 2014 World Club Challenge 36–14 win over the Wigan Warriors at SFS. On 17 June 2014, Mortimer joined the Gold Coast Titans mid-season on a 2-and-a-half-year contract. Mortimer played in 7 matches and scored 1 try for the Sydney Roosters before moving to the Gold Coast. In Round 15 of the 2014 NRL season against the St George Illawarra Dragons, Mortimer made his club debut for the Gold Coast Titans, kicking a goal in the Titans 19–18 loss at Cbus Super Stadium. In Round 24 against the Dragons, Mortimer played his 100th NRL career match in the Titans 34–6 loss at Jubilee Oval. Mortimer finished off his mid-season transfer year with the Titans with him playing in 11 matches and kicking a goal.
2015
On 31 January and 1 February, Mortimer played for the Titans in the 2015 NRL Auckland Nines. He finished off the 2015 season having played in 17 matches and kicking 2 goals for the Titans. On 26 September, he played for the Prime Minister's XIII against Papua New Guinea, playing off the interchange bench in his team's 40–12 win in Port Moresby.
2016
On 29 January 2016, Mortimer was named in the Titans 2016 Auckland Nines squad. Mortimer was also named captain of the Titans for the tournament. In Round 3 against the Wests Tigers, Mortimer scored his first club try for the Titans in their 30–18 win at Cbus Super Stadium. After sustaining a hamstring injury and the signing of Nathan Peats from the Parramatta Eels, Mortimer struggled to break into the Titans first 17 squad. Mortimer finished the 2016 NRL season with him playing in 7 matches and scoring 1 try for the Titans. On 5 November 2016, Mortimer signed with the Cronulla-Sutherland Sharks as being one of the potential replacements for the recently retired Michael Ennis at Hooker.
2017
He only played twice for the Sharks when in late June, he moved to England to play for then Super League side Leigh Centurions playing his first game on 7 July against Warrington Wolves.
2018
On 11 November, Mortimer announced his retirement from rugby league at just the age of 29. Mortimer wrote on Instagram "I've been so damn lucky to live my dream. It has been an amazing ride. Cannot wait until the next chapter... whatever that may be".
Personal life
As of 2019, Mortimer has become a teacher at Pimpama State Secondary College, Queensland, Australia.