He will remain in place until a replacement has been found.
Barry Jenkins, chairman of CEA, said: 'John has successfully led the Association for 17 years and his contribution to the smooth running of cinema exhibition is greatly appreciated by all members. The association will continue to develop on the sound base built by John.'
Wilkinson added: 'I have been most happy working with the members and wish them and my successor continued success.'
Before joining CEA, Wilkinson was Secretary to the British Chamber of Commerce and a divisional director of a management consultancy company.