The Puritans say they tried to change the 38-year-old’s mind after he told them he plans to step down.
But they were unable to convince him to remain and the boss who took them to promotion a year ago has left his position.
Chairman Ronnie Johnson accepts the news will be hard to digest for fans.
But he explained that he did everything he could to convince Whing not to walk away.
He told supporters that a new manager is now a matter of urgency as they plan for another National League North campaign.
“This will be upsetting news to the Puritans faithful and I would like to assure our supporters that we have attempted to change Andy’s mind, giving him time to reconsider his decision,” Johnson said in a statement.
“Whilst bringing many exciting and enjoyable moments, the significant step up to The National League North, with its requirements and expectations, alongside rapid growth of the club, has been challenging and a learning curve for us all this season.
“The board respects Andy’s decision and we would like to go on record to thank him for his hard work and commitment during the last three years.
“Banbury United has seen the most successful period under Andy’s management. Andy’s first year was disrupted by Covid pandemic measures and he then went on to take the team to promotion to Step 2, to play football at our highest ever level.
“From all involved at the Club, we can only echo the immense gratitude that is regularly expressed by our great fan base. We wish Andy success in whatever he decides to do in the future.
“Andy and the Whing family will always be welcome at Banbury United Football Club, where he will enjoy our affection as the Club’s most successful manager to date.
“The current focus of the board is to urgently recruit a replacement manager, in order to prepare for a successful 2023-24 season.
“Andy’s departure has undoubtedly added a short delay to player retention and recruitment plans and we will be working at full speed to build a team in good time for the opening of the National League North player registration window.”