The engineering group gave no reason for Mark King’s exit, but a spokesperson later said he was leaving at the end of June for personal reasons.
“He is taking a break after a number of years in a high-pressure job,” she said.
King, who has worked for the company since 1986, will later this month start handing over responsibilities to Tony Wood, who is currently head of the smaller marine division.
The aerospace business made up almost three-quarter of Rolls-Royce revenues last year.
King spent time working for Rolls-Royce in the UK, the United States, Australia and Switzerland.
The firm refused to comment on whether King’s departure is linked to an ongoing Serious Fraud Office investigation into claims of bribery in Indonesia and China.
Jefferies analyst Sandy Morris said King was “a highly regarded member of the management team ... reflected in the perceptions of investors and analysts alike”, adding his departure was “not going to pass unremarked”.
Rolls-Royce also confirmed yesterday that the head of its ethics committee, Ian Strachan, has stepped down from the board, as announced in February.
He will be replaced on the committee by non-executive director and BP’s head of refining and marketing Iain Conn.
Rolls-Royce hired City lawyer and litigation specialist Lord Gold in January to independently review the company’s ethics procedures.
The board declined to comment on the progress of the SFO probe at yesterday’s annual meeting. Some of the allegations refer to deals done a decade ago.