The 21-year-old from Horsham made his debut in the championship in 2011 with Arden, before moving to iSport for the 2012 season.
He scored his breakthrough win at Monaco this year, finishing 11th in the standings.
Carlin made its GP2 debut this year and completed a promising season on its way to fifth place in the teams' championship.
"I'm very happy to be racing for Carlin in 2013," said Palmer. "The team showed good pace this year in their second season in GP2 and they are hungry to build on that next year.
"My aim is to be fighting for the championship and I'm confident we are in a position to do that."
Palmer will race alongside Brazilian Felipe Nasr.
Team boss Trevor Carlin added: "Jolyon is a very promising young British driver and we're delighted to be able to welcome him into our GP2 team.
"He put in some fantastic performances last season and I believe he will be a regular race winner and title contender next year.
"With Jolyon and Felipe we have an exceptionally talented team, and preparations are already underway for a strong start to the 2013 season."