Dr Dhanuson Dharmasena, 31, from the Whittington Hospital in North London and another man Hasan Mohamed, 40, are to be charged in connection with an incident following a birth at the hospital in 2012.
It is alleged that the doctor carried out the procedure after being encouraged and aided by Mr Mohamed.
Announcing the prosecution, Alison Saunders, Director of Public Prosecutions, said: “The CPS was asked to consider evidence in relation to this allegation of female genital mutilation (FGM) by the Metropolitan Police Service.
“It was alleged that following a patient giving birth in November 2012, a doctor at the Whittington Hospital, in London, repaired FGM that had previously been performed on the patient, allegedly carrying out FGM himself.
“Having carefully considered all the available evidence, I have determined there is sufficient evidence and it would be in the public interest to prosecute Dr Dhanuson Dharmasena for an offence contrary the Female Genital Mutilation Act 2003.
“I have also determined that Hasan Mohamed should face one charge of intentionally encouraging an offence of FGM and a second charge of aiding, abetting, counselling or procuring Dr Dharmasena to commit an offence.”
She added: “Dr Dharmasena and Hasan Mohamed will appear at Westminster Magistrates’ Court on 15 April.”
Prosecutors said they had also looked at four other cases – one of which was new and three that were reconsidered after decisions to take no further action – and found there was insufficient evidence to bring charges.
One of the old cases involved a man calling an FGM helpline, intended for victims, to ask for the procedure to be carried out on his two daughters.
The new case involved two parents accused of taking their daughter abroad to have FGM.
The CPS would not give details of the other two cases.
FGM has been a criminal offence since 1985, and in 2003 the maximum sentence was increased from five to 14 years in jail.
One report indicated last year that as many as 100,000 women in Britain have undergone the illegal operation, with medics in this country offering to carry out the procedure on girls as young as 10.
John Cameron, NSPCC Head of Child Protection Operations, said:
“This is great news for the fight against FGM. The fact that we hadn’t previously had a prosecution in the UK for this child abuse despite it being a crime for almost 30 years is unacceptable.
“Today’s announcement by the Crown Prosecution Service sends out a strong message that they are taking FGM seriously.
“FGM is a public health issue that needs increased collaboration from professionals across heath, education and the police. We urge anyone who is worried about a child or wants support or advice to call our FGM helpline on 0800 028 3550.”
Commander Mak Chishty from the Association of Chief Police Officers said: “Across the country, police are working extensively to investigate and build strong cases against those suspected of inflicting or aiding or abetting female genital mutilation (FGM).
“Today’s charging decision demonstrates how much gravity the police, prosecutors and government places on ending FGM.
“Female genital mutilation is a barbaric crime that has no place in modern day Britain. The police are committed to working closely with health services, schools, colleges, social services and third sector organisations which have an understanding of this form of abuse and can help us reach those who may be at risk.
“Prosecutions of those who continue this horrific and outdated practice should signal a warning to those who’ve committed or are considering inflicting female genital mutilation as well as anyone who assists them or stays quiet when they know this abuse been committed; we are pursuing offenders and working to bring them to justice so that we can protect victims – some of them painfully young - and stamp out this appalling crime.”