Bowdler, the outgoing chief executive at Johnston Press, had announced last year that he would be stepping down in 2009.
Fry, who has been chief executive at Norwich-based Archant since 2002, will move into his new position from 5 January 2009.
Bowdler said: "I am delighted that the board has appointed John Fry as my successor. Since he arrived at Archant in 2002 I have greatly admired his abilities and achievements.
"He is ideally equipped to be the next chief executive of Johnston Press and it will be a pleasure to hand over the reins to someone for whom I have such a high regard."
Fry comes into the role with a raft of experience both in and out of the media sector and he is well respected for his work at Archant – a smaller company than Johnston Press.
For nine years Fry was UK, Europe, Middle East and Africa president at information company Dun & Bradstreet and spent four years as a consultant with Bain & Company.
He started his career with Procter & Gamble and is a graduate of Jesus College, Cambridge (MA Physics and Mathematics) and also holds an MBA from INSEAD where he won the Ford Prize for the top student in his year.
Fry said: "I am extremely excited to be joining Johnston Press and relish the opportunity to build on the success of Tim Bowdler and his team. The company has a strong local media franchise covering large parts of the UK and Ireland which I look forward to developing in both print and digital formats."
Roger Parry, chairman of Johnston Press, added: "We are delighted to appoint John as new chief executive. The board started the recruitment process many months ago and we have seen a large number of candidates from both inside and outside the regional media industry.
"John has done a tremendous job at Archant and has exciting plans for developing regional media. The whole Johnston team looks forward to working with him."
Archant's Fry confirmed as next chief exec of Johnston Press
Newspaper publisher Johnston Press has confirmed that Archant chief executive John Fry has signed a contract to replace Tim Bowdler.