New Zealander McNicholl scored on his debut in the 38-29 victory over Leinster after arriving in Llanelli last month from Canterbury.
The ex-Crusader scored seven tries in 14 Super Rugby appearances and could return before the end of December.
The 26-year-old is likely to miss European Champions Cup double-header matches with Toulon.
A Scarlets statement said: "Johnny McNicholl had emergency surgery on Monday afternoon for an acute medical complaint.
"It is anticipated that his recovery will be uncomplicated and he will be available for selection later this month."
Scarlets face back-to-back matches against Toulon on 11 and 18 December before playing Ospreys in Swansea on 27 December and Blues at home on New Year's Day.
McNicholl, who has a two-and-a-half year contract with the region, was included in the Scarlets' European squad even though he was not with the region for their opening matches against Sale Sharks and Saracens.
Scarlets wing Johnny McNicholl will be sidelined after undergoing "emergency surgery" on Monday.