The Vanarama National League Quakers confirmed on Sunday that the pair would be staying on for the rest of thre season.
The were given the nod after Martin Gray resigned to take over at York City.
But in another twist, they have decided the job is not for them.
A club statement read: "Darlington Football Club regrettably have to announce the departures of joint managers Brian Atkinson and Sean Gregan.
"Following consultation with the National League and the boards of Darlington Football Club and Darlington FCSG, Brian has been told that he must stand down from his role at Darlington FC because of a conflict of interest with his role as a director at the Martin Gray Football Academy.
"Sean has decided to leave because he was looking for greater security than the club could offer through a contract until the end of the season.
"We would like to thank Brian and Sean, who like the club are understandably very disappointed, for their service over the last five years. Both of them have played a key role in the club’s success, and we wish them all the best for the future.
"In the interim, senior players Phil Turnbull and Gary Brown will take charge of the team whilst we search for a new manager."