McNaughton, who has been on loan at Bolton Wanderers this season, joined Cardiff from Aberdeen in 2006 and helped the club clinch promotion from the Championship back in May.
He told the club's official website: "I think I'm part of the furniture now, I've been here a while!
"It's great really to look forward to another season at the club.
"When I first came we were playing at Ninian Park and everything has changed since then with excellent training facilities and the stadium.
"Obviously now we're a Premier League football team, looking to stay there."
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