The new deal will keep the 21-year-old at the Britannia Stadium until the summer of 2013.
The defender told the club’s official website: “I am delighted to sign the new contract.
“There has been some interest in me, but the manager wanted to keep me here, he has shown great faith in my ability, and I certainly wanted to stay here.
“I am still young and I still have a lot to learn in the game, and there is no better place to do that than at Stoke.
“The manager has told me to keep working hard at what I’m doing, whether that’s here or if I get another chance to go out on loan. It is, after all, important for me to play games and gain more experience.”
He added: “I feel I have improved a lot in my time at Tranmere and then last season when I was at Barnsley.
“I haven’t done anything at Stoke yet and it is my ambition to put that right in the future.
“But I know how difficult it is going to be – you just have to look at the quality of defenders in the squad to appreciate that.”
Stoke’s chief executive Tony Scholes said: “Ryan is one for the future and we are delighted with the progress he is making.
“While a considerable amount of attention has been focused on the major signings that we have made during the summer transfer window, the development of our younger players is also vital to the club’s future.”