The 33-year-old's loan deal from York expired at the end of December but he has completed a permanent return in time to face Fleetwood.
Carlisle spent last season at Sixfields but joined York in the summer.
"I am delighted to have Clarke on board," boss Aidy Boothroyd said.
"He was a key part of us staying up last year and he is a leader, he has plenty of experience and he is a superb addition to the squad.
"He is the sort of player and the sort of person who inspires and improves others around him and I am delighted he will be spending the next 18 months with us."
The former Burnley defender made five appearances for the Cobblers during his loan spell, with his last coming in the 2-0 win over Aldershot.