Eaden leaves the club at the foot of the National League North table with just two wins all season.
A statement on the club's website from new chairman Nick Hawkins reads: “With a heavy heart, myself and Nicky have agreed, that a change of direction is best for Nuneaton Borough Football Club at this time.
"Nicky and his team have worked in difficult circumstances throughout his tenure and I appreciate, as do the fans and players alike, his efforts and commitment to the cause.
“On behalf of the club we wish Nicky every success in his future, he has so much to offer and I know in better circumstances he will excel. I trust the Boro’ faithful will be fully behind us and continue to give Lee and the team the support that they have shown in previous matches.”
Following a departure, Eaden posted a heartfelt message to the Borough supporters on his Twitter page.
He said: "Just like to say a big thank you to the Nuneaton Borough fans for being so supportive! After a while my only concern was for the survival of the club for the fans and the welfare of the players! Wish the club all the best for the future! #uptheboro"
Assistant manager Lee Fowler will take charge of the first-team ahead of their FA Trophy game with Brackley Town tomorrow afternoon.