The society says it has reluctantly accepted his resignation and will make further announcements regarding his replacement.
A statement from the society says: “We are disappointed to see him go but wish him all the best for the future.”
Haggerty was appointed managing director of Skipton on January 1 2008.
Reporting to chief executive John Goodfellow, he had responsibility for the trading performance of the society. He was also an executive director on the society board.
Prior to his appoint as managing director, he was group commercial director, with responsibility for a number of the group’s subsidiaries, such as Baseline Capital, Pink Home Loans and Homeloan Management.
He joined the group as head of operations for HML in 1990 and prior to that had spent 17 years at Bristol & West.