Pete Clifton, left, a former editor of the BBC news website and head of editorial development at the corporation, will take up the role on 1 January.
Jonathan announced earlier this year that he would be stepping down as editor after 14 years in the role and 36 years with the company.
The appointment marks a return to PA for Pete who worked for the agency as chief sub-editor of PA Sport and editor of PA’s Teletext service in the mid-1990s.
Said Pete: “I am thrilled to have this opportunity to lead the PA’s editorial operations. As someone who has worked for PA and also been a customer, I am passionate about its reputation for fast, fair and accurate journalism.
“I look forward to helping PA prosper at the heart of the UK’s media landscape in the digital age.”
PA managing director Tony Watson added: “Pete Clifton has a reputation in the industry as an editorial heavyweight and we are delighted to have appointed him to this key position.
“He will bring to the role an impressive combination of editorial judgement, digital insight, and the leadership qualities to bring about the changes necessary to remain relevant in a rapidly evolving media market.”
In his 15 years at the BBC Pete also worked as head of news interactive, launch Editor of BBC Sport website and editor of Ceefax.
His most recent role was as executive producer for MSN in the UK where for the last three years he led a 70-strong editorial team.