But despite only leaving the Chairboys on May 26, he has already secured a return to football with Northampton.
He replaces Colin Calderwood, who quit Sixfields to take charge of Nottingham Forest.
Cobblers chairman David Cordoza said: "John is a terrific appointment for us. We had a number of high quality applications, and everyone we spoke to conducted themselves very well and put forward their own cases strongly.
"What impressed us most about John was what he brings to the job. He has a wealth of knowledge and experience, and he has countless contacts at all levels of the game."