The club confirmed in a statement that it had accepted the resignation of Stuart Mellish, who was only appointed at Shawbridge in the summer.
The statement said: "The board are grateful for the time and effort that he has committed to Clitheroe FC in the time that he has been with the club, and the directors wish him well in any future position that he takes.
"There will be more announcements once the situation has been further assessed."
Mellish's last game in charge was the 5-3 home defeat to Atherton Colleries on Tuesday, where they threw away a 3-1 half-time lead.
They also conceded five on Saturday, losing 5-2 at home to Mossley in the FA Cup, and currently sit 17th in the league table with three points from five games.
The club has since confirmed that Lee Ashforth will be taking over as caretaker manager, assisted by former Liverpool midfielder David Mannix.
Ashforth said: "We will pull together as a squad and see what the future holds after a difficult day. We have a great group of players and both myself and Dave will be doing everything we can to get three points this coming Saturday."
Clitheroe host Colwyn Bay in the league on Saturday (3pm kick-off).