The 27-year-old centre-back has committed his future to the Italian club until 30 June, 2023.
Koulibaly has been heavily linked with Chelsea for much of the last year and Maurizio Sarri's move to Stamford Bridge encouraged talk that he could follow him to the Premier League.
Napoli president Aurelio De Laurentiis claimed in August that he had rejected three €90 million ($143.1 million) offers from English clubs for a player he considers to be "the best defender in the world, probably".
It has been speculated there could be a release clause in the region of €100 million ($159 million) in Koulibaly's new deal, although Napoli did not disclose any such details.
The Senegal international has made 125 appearances in Serie A since signing from Genk in 2014, scoring eight goals.