The Holland international is facing up to several weeks on the sidelines after suffering knee ligament damage.
Huntelaar picked up the knock after colliding with his own goalkeeper during a 2-1 victory over Borussia Dortmund on Saturday.
Having found himself back among the goals against the reigning Bundesliga champions, a spell on the treatment table comes at a bad time for the forward.
Schalke will also be cursing their luck, as they prepare to enter a potentially pivotal run of games.
They are pushing hard for a top-three finish domestically and face Galatasaray on Tuesday in the second leg of a UEFA Champions League last-16 encounter which is locked at 1-1.
Huntelaar's absence will be keenly felt in crunch clashes, but Schalke can console themselves in the knowledge that he will not require surgery.
Club captain Benedikt Howedes told Westdeutsche Allgemeine Zeitung: "Klaas-Jan Huntelaar is going to be out due to injury. Fortunately he will not need to undergo surgery.
"We as a team hope to see Huntelaar recover quickly and we hope to have him back soon."