Charnley, the club’s managing director, had stayed on for a handover period following last month’s £300million takeover by a consortium led by Amanda Staveley, who is now looking to appoint a new chief executive officer.
"To have been at Newcastle United for 22 years has been an honour and a privilege, and the club, its people and our city will always be very special to me,” said Charnley, who club secretary before his appointment as managing director seven years ago.
"As it enters a new chapter in its history under new owners, I wish Amanda, the rest of the board and everyone connected with the club every success."
Staveley said: "I would like to thank Lee sincerely for his support and professionalism during this time of change. His knowledge and assistance have been hugely appreciated by the club’s new board.
"Lee ends a long association with the club and on behalf of the Board, staff and players, I’d like to wish him the very best for the future."
The club was sold by Mike Ashley to the Public Investment Fund, PCP Capital Partners and RB Sports & Media. The club’s new board “will continue to oversee all operations”.
Charnley’s departure comes before new head coach Eddie Howe’s first game in charge, the home fixture against Brentford tomorrow.
Charnley had appointed Steve Bruce, Howe’s predecessor, two years ago following the departure of Rafa Benitez.