The 21-year-old Academy graduate made his Sky Blues debut in 2009 and has now amassed 91 appearances, including eight starts this season.
Clarke's new deal comes after boss Steven Pressley told him over the summer that he was surplus to requirements at the League One club.
"In football, at times you love to be proved wrong and that is just the case with Jordan," Pressley said.
"I said to him in the summer that his future lay away from this club and the normal reaction is disappointment and in some cases players just down tools, but Jordan's reaction was the complete opposite.
"Of course he was devastated when I gave him the news but it put the bit between his teeth and nobody could be happier than myself that he's gone out and proved me wrong.
"I've been delighted with his contribution and his attitude, and long may that continue. He's got terrific attributes - he's quick, he's terrific in the air and he's also a very positive influence around the training complex and I look forward to continue working with him."