Parker, who has been an executive director since 1993, will leave the publishing group on Monday July 26 by mutual agreement.
Sly Bailey, chief executive of Trinity Mirror, will assume responsibility for the regional division after his departure.
Bailey said: "I would like to thank Stephen for his tremendous dedication, application and achievement in his time with the company. He has been involved in leading the business over the last 20 years as it has grown from being a small provincial publisher into the UK's largest newspaper publisher."
Parker led the Trinity through its integration of the Scottish and Universal Newspaper's acquisition in the early 90s, through to the building of Trinity Mirror as it is today. He said: "It has been a challenging, exciting, demanding and personally very rewarding experience."
Parker's departure comes just months after Piers Morgan, editor of the Daily Mirror, Trinity Mirror's flagship paper, was forced to resign following the publicaton of photographs, purporting to show Iraqi prisoners being tortured, which turned out to be fake.
Last month, Liz Hamilton, Trinity Mirror group agency manger for the Sunday Mail and Scottish Daily Record, left the company to join Capital Radio Group.
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