Barton leaves the Lancashire side 10th in League One, three points off the play-off places, with the Cod Army winless in their last four matches.
A short statement on the Fleetwood Town website read: "We would like to thank Joey for his work during his time at Highbury Stadium and wish him success in the future."
Barton at Fleetwood
The 38-year-old was appointed the role in April 2018 and his time in the north-west was filled with various incidents.
His first season was remembered by an alleged clash with Barnsley manager Daniel Stendel after his sides 4-2 defeat at Oakwell in April 2019.
In the following 2019-20 season, Barton guided Fleetwood to the League One play-offs. They were knocked out by the eventual play-off winners Wycombe Wanderers in the semi-finals.
After some impressive results this season, including their 4-1 win over Hull City in October 2020, the Cod Army have struggled to live up expectations with the ability in their squad.
Poor performances and questionable tactical decisions over the Christmas period are perhaps the reason Barton has lost his job early in 2021.
Fleetwood will have plenty of time to bring in Barton's replacement as their next League One fixture isn't until the 16th January at home to Portsmouth.
Following that, successive games against struggling sides MK Dons, Wigan and Northampton will be a test to see if the current Fleetwood squad has what it takes to get back into the play-off places.