The 27-year-old has been in the treatment room for a couple of weeks and missed the side’s 2-1 home defeat to Koln.
Schalke have confirmed the Ghanaian international will not be involved again this year and will undergo surgery to correct the problem in his right ankle.
The injury has persisted and has traveled to Munich to undergo treatment. Boateng joined the Royal Blues from Italian giants AC Milan but has struggled to keep fit due to the recurrent injuries.
The setback is a killer blow to any wild ambitions of representing Ghana at next year’s Africa Cup of Nations in Equitorial Guinea.