He is replacing outgoing CEO Tim Bowdler, who is set to retire in May after 15 years at the group.
Previously at Norwich-based regional media group Archant for six years, Fry has also held the position of president at information company Dun & Bradstreet.
The Cambridge University graduate faces a tough 2009 with Johnston Press, which at the end of last year was forced to freeze staff pay into the New Year due to a significant downturn in the advertising market in November.
Bowdler, chief executive at the time, said the decision was necessary to "help safeguard the future of our companies".
Johnston Press predominantly publishes local newspapers but it also prints more than 1m copies of The Sun each night at its Portsmouth and Diddington super plants and owns The Scotsman and Yorkshire Post titles.
The board of Johnston Press issued its thanks to Bowdler for his "major contribution" to the group and wider regional newspaper publishing industry.
Fry takes over the helm at Johnston Press
The New Year has seen a change at the top for Johnston Press, with John Fry taking over as chief executive of the regional publisher this week.
