The club have announced that the Scot has agreed to leave the Latics after a meeting with owner Dave Whelan less than six months after taking over the Championship side
Coyle took over as manager in June, following the departure of Roberto Martinez to Everton, but has seen the Latics lose their last three games including a 3-1 defeat to Derby County on Saturday.
Wigan are currently in 14th place in the Championship table, yet just six points off the play-off spots, and Coyle has revealed his disappointment at his exit.
“It is with great sadness that we have made this decision and I would like to thank all my football staff and the staff at the club, who have been very supportive of me in my time here,” he told the club’s official website.
“I am confident that with this set of players, the team can keep moving in the right direction.”
Next up for the FA Cup holders is a visit from Leeds United on Wednesday with the club confirming former manager Graham Barrow and assistant manager Sandy Stewart will take charge of the side for that club.