Anyone who visits the Subway website, accepts cookies from the site and provides an email address, will be emailed a digital coupon featuring a QR code that can be presented at a Subway store for a free cookie.
Sacha Clark, marketing director for the Subway brand UK and Ireland, said: "Our customers are at the centre of everything we do and we want to thank and reward them for their loyalty in an innovative – and delicious - way.
"What better than cookies for cookies to show our appreciation?"
Messages asking web users to accept cookies have been a familiar sight since 2011, when an EU directive came into force that required websites to give users the option to opt out.
In December the European Commission relaxed its rules around cookies. Companies no longer need to ask for content for using "non-privacy intrusive" cookies, such as those which remember shopping cart history or filling in forms over multiple web pages.