The former Scotland international made 76 appearances for the Cobblers since moving to Sixfields from Nottingham Forest in 2005.
But the 36-year-old has failed to fit into the first-team plans of manager Stuart Gray, and has left he club with immediate effect.
"Eoin and I sat down and had a chat and at 36 I don't think he is too keen on carrying on his playing career," said Gray.
"He was out of contract in the summer and it made sense to make this decision now.
"I think he wants to move into the coaching side of things and we wish him all the best with that. I would like to thank him for all of his efforts at the club and wish him every success for the future."