McNaughton's 400th league appearance for Cardiff came in a goalless draw at Brighton & Hove Albion on 21 August 2012. McNaughton started over half of City's fixtures in 2012–13, as Cardiff finally achieved promotion to the Premier League. With his contract expiring during the close-season, the club has confirmed that McNaughton has been offered a new deal. On 5 July 2013 it was announced on the official Cardiff City website that McNaughton had signed a new one-year contract extension with the Bluebirds. On 7 March 2014, McNaughton signed a new one-year contract with the "Bluebirds".