On 26 May 2006, it was announced that he would be joining Football League Championship side Cardiff City on a free transfer. McNaughton quickly became an important part of manager Dave Jones's plans as he played in the left full-back position, and his form once again earned him a recall to the Scottish national team, although injury robbed him of the chance to take his place in the squad. During his second season at Cardiff, having switched to right-back, McNaughton played in all six matches of the club's run to the 2008 FA Cup Final, including scoring his first goal for the club on 27 January 2008 with a 20-yard volley in a 2–1 victory over Hereford United in the fourth round. His first league goal came just a few months later when he scored on the final day of the season against Barnsley in a 3–0 win.