The decision comes following Fleetwood’s 2-1 defeat to Charlton Athletic, which extended their winless run to six league games.
Brown took charge of the club in May 2022, taking on his first managerial role after a stint as a coach at Aberdeen.
He led the Cods to a 13th-placed finish last season but they currently sit 23rd, having picked up just one point this season.
Fleetwood’s statement read: “Fleetwood Town can confirm head coach Scott Brown has left the club with immediate effect.
“Following a difficult run of results the club reluctantly felt now is the right time to make a change to the first-team management.
“Assistant head coach Steven Whittaker will also depart and everyone at the club would like to place on record their thanks to Scott and Steven 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.”
Barnsley are due to lock horns with Fleetwood on October 28, by which time a new head coach will most likely be in place at Highbury Stadium.
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