The right-back has not made an appearance for the club since sustaining a bang on the head in an FA Cup defeat at Blackburn Rovers in February.
A club statement said: “Stoke City can confirm that Andy Wilkinson has been given a contract until December 31, 2015 to enable him to regain full fitness with the support of the club’s medical staff after sustaining an injury last season.”
Wilkinson, who has spent his entire career at his hometown team after progressing through the academy, was out of contract and had waved an emotional goodbye to fans at the end of last season.
The 30-year-old has made more than 190 first-team appearances since making his debut in 2001 and has had loan spells at Telford, Partick Thistle, Blackpool and Shrewsbury.
He is hoping to return to competitive action in January.