The Dutch goalkeeper signed for the club during the close-season but injured his shoulder during his debut against Sunderland last month.
He has been on the sidelines ever since, and Jol is not sure when he will be able to call on the 31-year-old again.
Stekelenburg has been able to take part in some aspects of training but his participation has so far been limited, amid concerns over aggravating the problem further.
"If it is not right in two weeks' time, then he will probably need an operation," Jol said.
"It’s already five weeks now, so it's certainly long term. He had a few injections in his shoulder and it's quite sensitive.
"He trains but when he stretches he feels a lot of pain, so we have to be very careful."
David Stockdale has deputised for the injured goalkeeper so far this season but has only kept one clean sheet as Fulham have made a stuttering start to the campaign.
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