The 26-year-old, a free transfer signing from Woking last summer, made 40 appearances as Rovers finished third in League Two to go up automatically.
"Last season the spirit around the place was the best I've experienced," Clarke told the club website.
"League One will be a step up for everyone, I can't wait to get started."
The length of Clarke's new deal has not been revealed.
He joins goalkeeper Steve Mildenhall, defender Daniel Leadbitter and striker Billy Bodin who had already agreed new contracts at the Memorial Stadium.
Defender James Clarke has become the latest member of Bristol Rovers' promotion-winning squad to agree a new contract with the club.