Clarke guided Rovers to promotion from the Vanarama Conference last season as the Pirates became the first club to bounce back into the Sky Bet Football League at the first attempt for 10 years.
The new deal for the 37-year-old was announced on Bristol Rovers’ official website, although the club did not specify the actual length of the contract.
Clarke said: “There was never any question of me not agreeing to sign a new contract, we just needed a little bit of time to iron out all of the details.
“Bristol Rovers is a great club with great supporters and I’m looking forward to building on the success we had last season and can’t wait for the new campaign to begin.”
Rovers chairman Nick Higgs said he was delighted Clarke’s new deal had been sorted before the start of the new campaign.
“The way he has conducted himself and gone about his business since he first took over as manager has made a huge impression on all of us and we are delighted to have such a well respected, and talented, young manager in charge of the team as we return to the Football League,” Higgs said.
“Darrell’s knowledge of football at all levels is second to none, as are his man-management skills, and we have every confidence in his ability to take the club forward following last season’s success.”
Clarke first joined Rovers in the summer of 2013, as assistant to John Ward, having won two promotions at Salisbury to take the Wiltshire side into the Conference.
He succeeded Ward as manager in March 2014 and, although he was unable to prevent Rovers’ relegation to the Conference, he took the club back into the Football League via the play-offs.