Wigan were relegated to the third-tier League One having dropped into the bottom three of the Championship as a result of a 12-point penalty imposed at the end of the season due to the club going into administration.
"It's with a heavy heart that I have decided to leave Wigan Athletic," Cook, who has been linked with the vacant manager's job at Bristol City, said in a statement https://wiganathletic.com/news/2020/august/Statement-Paul-Cook on the Wigan website.
"I have been immensely proud to have continued my long affiliation with Wigan over the past three years and I have worked hard to represent the club to the best of my ability, to develop individuals and also create a team and a work ethic which the town can be proud of."
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Cook took over in 2017 and led Wigan back into the Championship in his first season. The club have appealed against the 12-point deduction in the hope of avoiding relegation.
"It is well publicised that the club is going through an incredibly challenging period and, of course, we are all hoping a positive outcome can be found so this football club can write its next chapter under new ownership," Cook, 53, added.
"That has to be the main priority for everyone involved and I know the administrators are working hard to ensure the club can get through these difficult times and find new owners." (Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Ken Ferris)
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