On 22 February 2016, Thurston was part of the North Queensland side that competed in the 2016 World Club Challenge against Super League champions Leeds, starting at halfback, scoring a try and kicked 5 goals in the Cowboys' 36–4 victory and he was named the man of the match, being awarded the Graham Murray Medal. In Round 7, Thurston scored his 1000th point at 1300SMILES Stadium when he kicked a conversion against the South Sydney Rabbitohs as Cowboys went on to blow out the Rabbitohs in a 44–18 victory. On 6 May 2016, Thurston played for Australia against New Zealand, playing at five-eighth and kicking a goal in the 16–0 win at Hunter Stadium. In Round 11 against Queensland rivals the Brisbane Broncos, Thurston played his 250th club career match for the North Queensland Cowboys in front of a home crowd at 1300SMILES Stadium, where he kicked the winning field goal with 5 minutes remaining to achieve victory for the Cowboys, 19–18. He received man of the match honours at Full-Time. Thurston later in 2016 announced that he is likely to retire at the end of the 2018 season.