The 20-year-old is on loan at Anderlecht but was injured during Friday’s 1-0 win over his former club Eupen and was taken off on a stretcher in the 78th minute.
Onyekuru cost Everton £6.8m in the summer. He has scored nine goals in 19 league appearances this season playing as a winger. His total haul is 10 goals in 28 games in all competitions.
However, scans on Saturday confirmed his worst fears that his season is over as he faces surgery and a lengthy rehabilitation.
“The medical staff of RSCA reports after extensive medical research that Henry Onyekuru has torn his medial bond,” Anderlecht wrote on their official website.
“Henry Onyekuru will soon be operated on. The medical staff is in close contact with his parent club Everton to determine where the Nigerian will go. Henry Onyekuru got injured against KAS Eupen on Friday.”
Onyekuru’s injury comes as a blow to Anderlecht, who sit third in Belgium’s top division. His injury also makes it highly unlikely that he will add to his Nigeria caps at next year’s World Cup in Russia.
Onyekuru featured in two Champions League games against PSG this season.