The 32-year-old striker has not played for Pools since January as the club initially attempted to deal with the problem with a series of injections.
He was Hartlepool's top scorer with 15 goals last season and had netted four times this campaign.
Head physio Ian Gallagher told the club website that Paynter is expected to be back for pre-season training.
Hartlepool captain Billy Paynter will miss the rest of the season after having surgery on an Achilles injury.