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The job at Bolton was Lee's first as a managerBolton have parted company with manager Sammy Lee by "mutual consent". Lee, 48, was promoted from assistant manager in April after the exit of former boss Sam Allardyce.
But he has had a difficult start to the current campaign as Bolton lie second from bottom of the Premier League with just one league win to their credit.
"This has been a difficult decision for all parties but we have agreed the time is right," Bolton chairman Phil Gartside told the club's website.
General manager Frank McParland has also left the club.
First-team coach Ricky Sbragia could now take temporary charge of the side who face a trip to in-form Arsenal on Saturday.
606: DEBATE Should Bolton have persevered longer with Lee?
Gartside added: "Sammy has played an important role in the club's recent history. We wish Sammy and Frank well for the future.
"Our efforts will now be to look for a replacement manager to concentrate on the future."
Lee became a coach at Bolton in 2005 and his managerial role at the club was his first after being involved in the coaching set-up firstly at Liverpool and then with England.
He has been embroiled in uncertainty over Gary Speed stepping down as first-team coach during the past week and how that came about.
Lee stated Speed had been relieved of his duties and the midfielder would be concentrating on his playing role.
But Speed, 38, insisted he chose to resign to regain his form and his place in the first-team after he was dropped for the recent 1-0 defeat to Chelsea.
There was lots of talk of a split in the dressing room and that he had lost the support of the players 5Live football reporter Juliette Ferrington
Bolton have made it through to the group stages of the Uefa Cup and face tough games against Bayern Munich, Red Star Belgrade, Aris Thessaloniki and SC Braga.
"According to Bolton Wanderers he has left the club by mutual consent," said 5Live football reporter Juliette Ferrington.
"But you ask yourself - would Sammy Lee have wanted to have left bearing in mind he kept talking about being a winner and that he wanted to get Bolton out of the position they were in.
"But it's fair to say he has had a shocking season with them and, to be honest, he was hanging on to his job by a thread after the events of the last week.
"There was concern from Phil Gartside with the way things were developing.
"There was lots of talk of a split in the dressing room and that he had lost the support of the players.
"We were led to believe that their next home game against Aston Villa was to be the crucial game but, obviously, the club have taken this decision during the international break."
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