The 58-year-old suffered a stroke in March and, on the advice of his doctors, will step aside in order to concentrate on his health and continue his recovery
Fry took the job in June 2013 but was taken ill in March this year and announced on Monday that he would step aside in order to concentrate on his health.
"As is now well known, I suffered a stroke on 4 March this year," he said in a statement on the Premier League's official website.
"I have been very fortunate and I am delighted to be making significant progress with my recovery. On the advice of my doctors, however, I realise that I need to scale back my business activities.
"It is with regret, therefore, that I have decided to step down from my position as chairman of the Premier League which... demands more commitment than I am able to give currently.
"It would not be fair to the Premier League, nor its member Clubs, not to be able to continue to give that commitment."
Bruce Buck, chairman of the organisation's Audit and Remuneration Committee, extended his gratitude to Fry and wished him well in his recovery.