Whelan, who was in the role for 20 years, has handed the reins to his grandson, David Sharpe.
The club confirmed the news in a statement on Tuesday, with Whelan, 78, explaining the move: "I am approaching 80 years old and spend an increasingly long time abroad, and cannot make it to games.
"It is a decision I have been mulling over for some years and I believe David is now ready.
"Contrary to some suggestions, there are no plans to sell the club, which will remain in family hands and I have every confidence that David, along with Chief Executive Jonathan Jackson, will lead us forwards with wisdom.
"In making this announcement, I would like to say huge thank you to the Board of Directors, all the staff at the club, and of course the wonderful supporters of Wigan Athletic, who have helped make the journey over the past 20 years such an exciting and memorable one."
Under Whelan's watch, Wigan climbed from the foot of the fourth tier to the Premier League, winning the FA Cup along the way in 2013.
However, they now sit in the bottom three of the Championship after being relegated from the top flight in the same year they experienced Wembley joy against Manchester City.
Whelan endured some controversy in what has transpired to be his final season at the club, earning a Football Association charge for using insulting language in a newspaper interview in which he made remarks that carried negative connotations about Jewish and Chinese people.
