Phil Halsall was suspended on full pay in August pending the outcome of a disciplinary investigation into a Â£5m tendering contract.
Mr Halsall, who took up the role in 2011, said the decision to leave "has not been an easy one".
The Labour-led council's leader Jennifer Mein said she wished him "the best of luck for the future".
Mr Halsall was neutrally suspended as chief executive while an investigation into the tendering of a fleet contract is being conducted.
The deal to run the council's fleet services was agreed in April by the former Conservative administration.
It was awarded to BT and One Connect Ltd, a partnership between BT and the council.
The continuing probe followed an independent review of the tender process.
Mr Halsall has denied any wrong-doing and has previously said he was "vigorously" pursuing his reinstatement.
He joined Lancashire County Council in 2009 as executive director of resources and took up the role of chief executive in 2011.
He said he had "enjoyed my time in Lancashire".
The suspended chief executive of Lancashire County Council has left the authority by "mutual consent".