The 33-year-old, who succeeded Simon Halsey at Winch's Field in May 2013, told the club's officials on Wednesday morning that he would be leaving after their trip to Whyteleafe.
Denly, pictured, kept Bay in the Ryman League in his first season in charge before guiding them to top half finishes in each of the next two campaigns. He is standing down with Bay set to finish in 17th spot, their lowest final berth since his first season at the helm.
The Kent club's officials confirmed Denly's departure after fours years at the helm in a statement on their website thanking him for his services after taking them to within touching distance of the promotion play-offs last season.
After Denly told the media how "proud" he'd been to manage the club, the statement read: "Sam gave an exclusive interview at lunchtime today in which he said that it had been one of the hardest decisions he had had to make.
"He was very proud at being given the chance to manage at Herne Bay and proud of what had been achieved and Herne Bay Football Club would like to thank Sam for his efforts at the football club and what he has achieved. The club wishes him well for the future."
Image courtesy of www.hernebayfootballclub.co.uk
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