The 43-year-old will take up his position on July 3.
A Wigan fan, Jackson already has a link with the club as he is the son of former president Stan Jackson - the man who persuaded Dave Whelan to take over as chairman in 1995.
"Jonathan is somebody I have known for a long time through his father and his long association with the club," said Whelan.
"He is Wigan Athletic through and through and has an impeccable management track record.
"I believe he is the right man to take the club forward and I'm looking forward to welcoming him on board."