The Peru international was limited to 19 Bundesliga appearances, but still had a hand in 16 goals, scoring nine and providing another seven assists.
A close-season full of physiotherapy in an attempt to be fit for the upcoming campaign has seemingly failed, though, and Farfan was not present as Schalke returned to training on Tuesday.
And the club's general manager Horst Heldt expects Farfan to now require an operation to return to fitness.
Heldt told the club's official website: "It is assumed that Jefferson needs surgery on his knee.
"We have first tried at his request, to treat the injury conservatively. Jeff had worked during the summer break in Peru a physical therapist from Germany and this has brought with it daily intensive.
"In this case, however, the desired effect is not arrived. At present we assume he will be missed for a long time."
Schalke coach Jens Keller's attacking options have been boosted into the new season with the singing of Sidney Sam, who trained with his new team-mates for the first time this week.
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