The former Manchester United player recently experienced a heart rhythm disorder, something which is not considered serious but did require surgery.
"On Tuesday morning, Scott McTominay underwent an ablation procedure at Spire Manchester Hospital. The operation was a complete success," the Serie A club said in a statement.
"McTominay will rest for two weeks and then resume training."
McTominay, 29, has been a key player for Napoli since joining from Manchester United in 2024, scoring 27 goals in 82 matches.
But he was off-form in their opening two Serie A games.
Napoli previously said that McTominay would miss Scotland's upcoming Nations League fixtures against Slovenia (twice), Switzerland and North Macedonia.
Napoli, who have just three points from their opening three Serie A games this season, host Arsenal in the Champions League on Wednesday and then play Bologna and Fiorentina before the international break.