The 55-year-old, who is now tied down to the club until 2021, has been in charge of the League One outfit for the past five months.
"Pompey is a really special, incredible football club," the manager told the club's official website. "The chairman, board and CEO all share a long-term vision of where the club is going and I want to be a part of that.
"When offered the opportunity to extend my contract it was a very simple decision to make and I am extremely excited about the future of PFC."
Chief executive Mark Catlin added: "We were absolutely thrilled to be able to bring Kenny to Pompey this summer and with his fantastic work ethic and experience, the club continues to progress alongside many of the individual players in the squad.
"Kenny has bought into the project for the future of the club. We're happy with him and he is happy here – it's a great match for both parties."
Portsmouth have won their last three games on the bounce.