The 29-year-old clocked up just under 200 appearances for the League One side since initially joining on loan in 2008 and was a free agent after his contract expired.
"I was massively impressed with this club from the first moment," he told the club's official website.
"Joining Fleetwood is an exciting prospect and I jumped at the chance after seeing the plans and hearing the chairman's vision.
"I'm an ambitious person and an ambitious player. The manager and chairman have shown me this club is geared to success and I want to play my role in that success with Fleetwood Town."
The centre back played for the likes of Northwich and Accrington before helping Boro to double promotions.