The Peru international was injured in their 1-0 win at Basel in the European competition on Wednesday.
"Adductor muscle fibre tear. Farfan will not be available for Schalke in the coming weeks," the club said on Twitter.
Schalke, already without long-term injured striker Klaas-Jan Huntelaar and central defender Kyriakos Papadopoulos, are languishing in 14th place in the Bundesliga after seven games.
They are, however, top of their Champions League Group E with six points following two wins in two games.
(Reporting by Karolos Grohmann; Editing by Alison Wildey)
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