Former Manchester United player McTominay has developed a "mild, benign arrhythmia," a condition that causes irregular heartbeat, the Serie A side said in a statement.
"Scott McTominay is due to undergo corrective ablation surgery (PFA) in the coming days. The player will be available again after the international break," Napoli added.
The 29-year-old is set to miss Scotland's four Nations League group matches, two against Slovenia and one each against Switzerland and North Macedonia, scheduled between September 26 and October 6.