Branthwaite has not played for Everton this season after sustaining an injury in pre-season. The England international was close to returning to the side after making great progress behind the scenes but has now suffered a major set back.
Everton released a statement on Monday afternoon, confirming that he will be out of action for some time.
"Following specialist consultation, it has been determined the defender will undergo a surgical procedure to address the issue.
"Branthwaite will commence a structured rehabilitation programme under the supervision of the club's medical team following the operation."
Everton turned down multiple offers from Manchester United for Branthwaite in 2023 before he signed a new five-year contract, tying him down to the side who are aiming to finish within a European spot this season.
The Toffees have conceded nine goals in their eight Premier League matches so far this season without Branthwaite as Moyes relies on experienced duo James Tarkowski and Michael Keane to lead the back line.
The 23-year-old missed 15 matches with a groin issue last season in what has been an injury riddled few years for the youngster, who cannot catch a break.