The 23-year-old has made 183 appearances for the club since arriving four seasons ago.
Assistant manager Paul Stephenson said: "We are delighted to have Dean on board for 2013/14, he is one of the longest-serving players here at the club and has a great attitude to his football. He will be a big part of what we do next year."
Winnard added: "It was an easy decision. Accrington is a great club and the way that [manager] James [Beattie] and Paul are preparing for next season is getting a lot of people here excited."