The new deal will keep the defender with the Potters until the summer of 2013.
Stoke manager Tony Pulis told Stoke’s official website: “It is important we look after the players who helped start off what we have achieved over the past three years and Danny is one of them.
“Although he has found it difficult to command a place in the squad this season, he is an excellent professional and every club needs players with his qualities who can be relied upon to come in and do a good job if required.
“The impact he has made at Preston is evidence of that and he will benefit from playing regular first-team football.”