Morgan had only penned a new deal with the Women's Super League side this summer after guiding them to the Championship title last term.
However, Leicester have lost their opening eight games in the 2021-22 WSL season, and the club have affirmed that "a change in leadership" is necessary for the remainder of the campaign.
A statement on lcfc.com read: "Leicester City confirms the departure of Jonathan Morgan from his role as LCFC Women First Team Manager.
"The Football Club would like to place on record its thanks to Jonathan for everything he has helped the club to achieve during his time as manager, which included promotion to the FA Women's Super League as FA Women's Championship winners.
"Retention of its FA Women's Super League status is central to the club's vision for the long-term development of women's football in the city. The club feels a change in leadership is now necessary to give the team the best possible chance of achieving this in the remaining months of the season."
Morgan - last season's LMA Championship Manager of the Year - added: "This club has been part of mine and my family's life for 12 years from when my sister Holly Morgan joined as a young player.
"To have taken Leicester from the Midlands Division 1 to a FAWSL club gives me nothing but pride. Earning promotion last season in the manner we did will always be a memory I can share with the fans and the city.
"This season has been disappointing, with injuries contributing to a difficult start, but we haven't achieved the results we had hoped for. I wish the club, the staff and the players my very best."
Emile Heskey - who scored 46 goals in 197 games for Leicester - will take first-team training ahead of the Continental Cup meeting with Manchester United Women on December 5. body check tags ::