The deal for the 33-year-old is initially a loan until the January transfer window opens.
Carlisle was an inspirational figure during a loan spell at Sixfields last season as the Cobblers avoided relegation.
"I am absolutely delighted to have Clarke back on board," said Northampton boss Aidy Boothroyd. "He was a huge part of the squad that stayed up last season. I am really pleased he has agreed to come here and to help us build on the good work we started last season and have carried on so far this season.
"Clarke is exactly who we need right now, he is exactly the right type of person and the right type of player. I am sure he will form a successful partnership with Kelvin Langmead, who I think has been outstanding so far this season. Those two know each other from last season and it is great to have them reunited."
Carlisle is available to make his second debut for the club in Tuesday night's home league fixture against Morecambe.