Lee Fowler, who stepped in when Nicky Eaden left last month, will not be staying at Liberty Way.
Nuneaton are bottom of the National League North, six points from safety.
They travel to face Darlington on Saturday looking for three points as well as a new manager.
Fowler has taken to twitter to thanks fans for backing him in his short spell in charge.
“My time has come to leave and I would like to thank the the players, the fans and the groundsmen,” he posted on social media.
“Been a fantastic experience the good the bad and the ugly. I’ve loved every minute off the process good luck to Nuneaton.”