The Crown Prosecution Service says it also looked at four other cases of alleged FGM - 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.
Prosecutors are considering another four cases of alleged FGM, and are in early discussions with police about another two.
The Director of Public Prosecutions explained the FGM charges were brought after receiving information from the Metropolitan Police.
Alison Saunders 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."
Dr Dhanuson Dharmasena has been charged with an offence contrary to the Female Genital Mutilation Act.
Hasan Mohamed will 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 of FGM.
Both men will appear at Westminster Magistrates Court on April 15.
Two men, Dr Dhanuson Dharmasena, from the Whittington Hospital in London, and Hasan Mohamed, will be charged in the first UK prosecution for female genital mutilation, the Crown Prosecution Service said today.