According to a statement today, Fry, who joined the company a little more than two years ago, has notified the board of his intention to step down by March 2012.
"The process is now being started to find John's successor and a further announcement will be made at the appropriate time," the statement added.
Fry was appointed chief executive of Johnston Press in January 2009, joining from Norwich-based regional media group Archant. He succeeded Tim Bowdler, who retired.
Johnston Press announced in March last year that Fry was paid £959,000 for his first year with the company, despite redundancies across the group and a pay freeze for all staff.
His pay included: a £210,000 cash bonus; a £210,000 performance-related bonus paid in shares (deferred for three years); and a basic salary of £525,000.
News of Fry's resignation comes as the company announces a drop of almost a third in pre-tax profits for 2010.
According to today's preliminary financial results for the year, pre-tax profit fell by 29.6 per cent from £43.3 million to £30.5 million. Overall revenue for the group fell 6 per cent from £423.7 million to £398.1 million.
Group chairman Ian Russell acknowledged that the group had made "a weaker start to 2011" than anticipated, and attributed the fall in profit to "improving systems and technology and making processes more efficient".