The 37-year-old will leave the Cobblers this summer, along with six others, after not being offered a new deal.
Former Hull and Bradford keeper Duke made 92 appearances for Northampton, including a loan spell in 2012, and signed permanently in 2013.
But Wilder admitted he wanted to bring in a younger keeper which would limit Duke’s playing time.
“You have to make decisions as a manager and we thank all the players for their efforts. They’ve been good for me and I think we as a club have been good to them,” he told the club’s official website.
“Matt Duke wants to play first-team football and I can’t guarantee him that. Matt has had a really good career but we want to bring in a younger goalkeeper and we are looking at possibly bringing in someone on a season-long loan.
“Matt wants to play and I can’t guarantee him first team football.
“It was a tough decision because I’ve known Matt for a long time but we are taking a long-term view with this decision.”
Darren Cater, Ben Tozer, Lee Collins, Ian Morris, Lewis Hornby and Ross Perry will also leave Sixfields.