David Carrick, 46, of Stevenage, Hertfordshire, was arrested on Saturday over an alleged offence in St Albans on 4 September last year.
Mr Carrick, who is based within the Met's Parliamentary and Diplomatic Protection Command, was charged with rape by Hertfordshire Constabulary on Sunday.
The officer was not on duty at the time of the alleged rape, the force said.
The force said it awaited the outcome of criminal proceedings and had referred the case to the Independent Office for Police Conduct.
Hertfordshire Constabulary said Mr Carrick remains in custody. He is due to appear over video at Hatfield Remand Court on Monday.
In a statement, Met Police commissioner Cressida Dick said: “I am deeply concerned to hear the news today that an officer from the Met’s Parliamentary and Diplomatic Protection Command has been arrested and now charged with this serious offence.
“I fully recognise the public will be very concerned too. Criminal proceedings must now take their course so I am unable to comment any further at this stage.”
Malcom McHaffie, the chief crown prosecutor of CPS Thames and Chiltern, said: "The CPS has today authorised Hertfordshire Constabulary to charge serving Metropolitan Police officer David Carrick, 46, with one count of rape following an alleged attack on a woman on the night of 4 September 2020.
“The defendant's first court appearance will take place via video link at 10am tomorrow at Hatfield Magistrates’ Court.
“The Crown Prosecution Service reminds all concerned that criminal proceedings against the defendant are active and that he has a right to a fair trial.
“It is extremely important that there should be no reporting, commentary or sharing of information online which could in any way prejudice these proceedings.”