The 29-year-old Scotland international underwent a planned ablation procedure at Spire Manchester Hospital following a diagnosis of a mild, benign arrhythmia last week.
"As was planned, Scott McTominay had an ablation procedure carried out at the Spire Manchester Hospital during the morning," Napoli said in a statement.
"The surgery was perfectly successful. McTominay will observe a rest period of around two weeks before resuming training."
The former Manchester United midfielder sat out Napoli's 3-2 Serie A defeat by champions Inter Milan on Saturday. He is set to miss Wednesday's Champions League opener against Arsenal, as well as league fixtures against Bologna and Fiorentina.
McTominay is expected to resume full training during the upcoming international break.