The 26-year-old centre-half made his Hibs debut in 2008 and has been a first-team regular for seven seasons.
He was a Scottish Cup winner in May, having been a losing finalist in 2012 and 2013.
"I'm determined to build on our success from last season and get Hibs back to the Premiership," said Hanlon.
Talking to the club website, he added: "There is a real excitement following the end to the season and, with [new manager] Neil [Lennon] coming in, I'm looking forward to getting started again."
Hibernian defender Paul Hanlon has signed a new three-year contract, keeping him at Easter Road until the summer of 2019.