Nana has not played since rupturing his cruciate knee ligament in the Cobblers' 3-0 win at AFC Wimbledon in September 2011.
The 22-year-old right-back has now made a complete recovery from the injury but his services will not be retained.
"I've spoken to Nana about his future and we won't be offering him a contract for next year," said manager Aidy Boothroyd. "We're a different club now to the one that he joined.
"Hopefully we can get him organised and help him find another club."
Boothroyd added: "He's always got a smile on his face, he works extremely hard but there'll be nothing here for him next year."
Nana, signed by former Northampton boss Gary Johnson two years ago, made 17 appearances for the club prior to his injury.