Benjamin Herman, now 79, was the personal assistant or “equerry” to the 93-year-old husband of Queen Elizabeth from 1971 to 1974.
A spokesman for the UK Crown Prosecution Service said Herman would appear in court on Monday.
“He is charged with three counts of indecent assault between 1972 and 1974 on a girl aged around 12,” the spokesman said.
Herman’s role was to attend to Philip’s engagements and personal matters, and he later became the head of the household of Philip’s daughter Princess Anne.
The Daily Mirror reported that police had examined Philip’s official diaries from the time and taken statements from former palace staff.
A police spokesman would not comment on whether former palace staff had been interviewed and a spokesman for Buckingham Palace declined to comment.
He said: “Officers from Wandsworth CID investigating an allegation of historical sexual assault which occurred between 1972 and 1974 at a location in Putney arrested a 79-year-old man.
“He was subsequently bailed to a date in mid-June pending further investigation.”
Britain has been rocked by a series of scandals involving historic child abuse by prominent figures.
The Mirror reported that the alleged victim had come forward following the 2012 revelation that the late BBC presenter Jimmy Savile was a prolific sexual predator, which sparked a wave of investigations.
Earlier this month the prime minister, David Cameron, vowed to leave “no stone unturned” in investigating accusations, including claims of a paedophile ring involving senior politicians in the 1970s and 1980s.