Barton guided Fleetwood to the League One play-offs last season, but his team lost to Wycombe in the semi-finals and failed to mount a strong promotion push this term.
Fleetwood are in 10th place in the third tier after one win in their last seven league games, with their next two matches postponed due to several positive tests for the coronavirus.
"Fleetwood Town can confirm manager Joey Barton has left the club with immediate effect," a club statement said.
"We would like to thank Joey for his work during his time and wish him success in the future."
Barton, 38, was appointed to his first managerial role in April 2018.
His maiden season in the dug-out was marked by controversy after an alleged clash with then-Barnsley boss Daniel Stendel following a League One match.
Stendel was said to have suffered a damaged tooth following the incident which occurred after Barnsley's 4-2 victory in April 2019.
Former Newcastle star Barton, whose playing career included an England cap in 2007, was due to stand trial last summer having earlier pleaded not guilty to a charge of assault occasioning actual bodily harm.
However, the case was put back to June 2021 because of coronavirus and the interruption to the 2019-20 season.
Barton's appointment raised some eyebrows given his playing career was marred by violent incidents.
In May 2008, he was jailed for six months over a late-night attack on a man and a teenage boy in the centre of his home city of Liverpool.
In July that year he was given a four-month suspended jail term for attacking his Manchester City team-mate, Ousmane Dabo, in training.
His playing career ended when he was banned for 18 months by the Football Association in 2017 after he was investigated for placing 1,260 bets on football matches between 2006 and 2016.
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