The Cod Army have lost all of their last five games and, having accrued only four points since September, are in the League One drop zone.
Grayson, who guided Leeds United to promotion to the Championship in 2010, took charge of Whites loanee Ryan Edmondson in his role as Fleetwood manager.
Under Grayson, the striker scored two goals in 13 appearances across all competitions and now the 20-year-old faces a mid-loan manager change for the second season in a row after Keith Curle left Edmondson's former loan club Northampton Town in February of the 2020/2021 season.
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Fleetwood announced Grayson's departure with a club statement on their website on Wednesday morning.
"Fleetwood Town can confirm Head Coach Simon Grayson has left the club with immediate effect," the statement read.
"Following a difficult run of results, Assistant Head Coach David Dunn will also depart and everyone at the club would like to place on record their thanks to Simon and David for their hard work and professionalism during his time at the club.
"The search for his replacement will begin immediately and we will issue a further update on the first team staff in due course."
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