The club suffered an early FA Cup exit, defeated at home by Radcliffe on Saturday, and have struggled for consistency early on in the National League North season.
The Yellows have lost five games so far this campaign, sitting on eight points leaving them in 18th place.
Beesley took charge of 139 Warrington games, winning 59 of them, and the club say he will always be remembered as the manager that led them into the division.
They are now hunting for a new manager after the 43-year-old fell on his sword after eight years of service.
A statement read: “Warrington Town can confirm it has accepted the resignation of Mark Beesley from his role as manager.
“Following discussions last night and this morning, his eight-year run as part of the club’s management team has come to an end.
“During his tenure, the club has grown with average attendances climbing from 547 in his first season to almost 1,200 last term.
“Everyone at the club would like to thank Mark for his contribution and wish he and his family all the best for the future.
“A further statement will be made in the next few days.”