The 24-year-old sustained a tendon injury in August and has featured just twice for Everton since joining from Bundesliga club Mainz.
Gbamin resumed light training earlier this month but suffered a setback on his return from injury and was operated on in France on Wednesday (AEDT).
A statement on Everton's official website read: "Everton Football Club can confirm that Jean-Philippe Gbamin has undergone surgery on a tendon injury in his right quadriceps muscle, which will keep the midfielder out of action for around three months."
Gbamin, signed as a reported £25million replacement for Idrissa Gueye, will continue his rehabilitation with Everton's medical staff at the Finch Farm training base.
Marco Silva's side are 18th in the Premier League following just two wins in their opening eight matches.