Jonathan, pictured left, joined the news agency as a general news reporter in 1979 and became its editor in 2000.
He will become editor emeritus from 1 January when his successor is expected to be appointed.
The recruitment process for Jonathan’s successor will start shortly.
As emeritus editor, Jonathan will be responsible for the agency’s coverage of the 2015 general election – the eighth he will have reported on for the PA.
Said Jonathan: “Being editor of the Press Association has been an immense privilege and enormous fun but I think it is time to let someone else have a go.
“At a time when there is a national debate about editorial standards the Press Association can be proud that its journalists are committed to the highest standards of robust, independent, ethical journalism.
“It is a tremendous honour to be appointed Emeritus Editor and to have the opportunity to help maintain that cherished reputation.”
Although he will formally retire on 22 May 2015, Jonathan will continue to be involved in the promotion of editorial standards and journalist training
Clive Marshall, PA Group chief executive, said: “Over his 36 years as a journalist and Editor with the Press Association Jonathan has made an immeasurable contribution to the Agency’s coverage of the stories that have dominated both the UK and global news agenda.
“At a time when our industry has experienced unprecedented scrutiny and criticism, Jonathan has ensured, throughout his tenure, PA has remained true to its core values of fairness, independence, impartiality and integrity.
“We all wish Jonathan a healthy and happy retirement, and I am delighted that we will continue to have access to his immense skills and expertise particularly in the support and training of our young and not so young journalists.”
Its executive director Bob Satchwell said: “Jonathan has been a rock for the media in the UK and beyond. Every part of the media owes him a debt of gratitude for his work at the Press Association and for being a steady hand on the tiller of the Society of Editors as president twice especially during the tumultuous year of 2012/13.
“His quiet, self-effacing style hides a powerful force in UK journalism.”