The former Mansfield Town manager has called it a day after two seasons at the club.
Cox took over at the National League North Poppies in October 2019.
He has managed to steady the ship but decided the time was right to say goodbye.
Experienced Luke Graham will take the team for Saturday’s match at Bradford Park Avenue.
A statement on the club’s website confirmed the departure.
The club said: “Manager Paul Cox has tonight resigned as Manager of Kettering Town Football Club.
“At very short notice, we are grateful to Academy Director,Luke Graham, and Technical Director,Alan Doyle, who will take charge of the team at tomorrow's game at Bradford Park Avenue.
“Further information will be released when possible.”