Wilson was appointed to the role in late 2010 and will be departing in September.
She said: ‘I came to the CIPR from a commercial background and always intended to return to a professional public relations role after three years. It’s still a big decision to go, but I am proud that across many areas, we have an institute that is stronger than when I took up the post.
‘I’ve worked with some amazing people and, after I leave, I will really miss my team here who have worked so hard to deliver the things we have achieved together. I remain totally committed to the job while I remain in post and to the goals we will set for 2013 and beyond.’
As CEO, Wilson led a number of reforms, including to the CIPR membership structure.
Most recently, the professional body overhauled its election processes.
This followed president elect Lionel Zetter stepping down from his role after complaints his nomination had been entered into last year's elections late.
Wilson's letter of resignation was received by Sue Wolstenholme, CIPR president.
Wolstenholme said: ‘Jane has made a real difference to the CIPR. Under her leadership, both staff and senior volunteers have been galvanised by a common sense of purpose. The CIPR is now in better shape than ever, offering access to high quality professional development opportunities and a membership structure that provides professional credibility and accountability.
‘I want to thank Jane for the contribution she has made and will continue to make to the future of public relations in the UK. We look to the future with confidence and will keep members informed about the appointment of a successor.’