The 42-year-old has opted to walk away from Highbury Stadium just 11 days before the start of the 2016-17 campaign.
The former Hearts and Rangers defender, who took charge of the Fishermen in October last year, ended last season with the club 19th in the table, five points above the relegated quartet.
This morning Fleetwood released a statement, which read: "Fleetwood Town can confirm we have agreed to accept the resignation of manager Steven Pressley.
"The decision was made this morning following a meeting with the 42-year-old where it was agreed it would be best to take the club in a different direction.
"Fleetwood Town would like to thank Steven for his professionalism and effort during his nine months at Highbury, particularly in successfully maintaining the club's League One status last season. Our focus will now turn to the prompt recruitment of a new manager to take the club forward."
Pressley, who was in charge for his side's pre-season 5-0 defeat to Liverpool a fortnight ago, has previous management experience at Hearts, Falkirk and Coventry City.