Dr Dhanoun Dharmasena is accused of re-performing an FGM procedure on a woman who gave birth at his hospital in November 2012 following damage caused by labour.
Another man, Hasan Mohamed, is accused of intentionally encouraging an offence of FGM, and of aiding, abetting, counselling or procuring Dharmasena to commit the offence.
It was not immediately clear what Mohamed's relationship to the victim was, but he is not a healthcare professional.
"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," said Alison Saunders, director of public prosecutions.
Both Dharmasena and Mohamed will appear at Westminster Magistrates' Court on April 15.
Some 100 to 140 million girls and women globally are thought to have undergone FGM, which ranges from removal of the clitoris to more widespread mutilation, and can lead to infection and long-term severe pain.
FGM has been illegal in Britain since 1985 but no-one has ever been prosecuted.
There have been increasing calls on police and the government to act, and last month ministers introduced a new requirement on British hospitals to keep a record of patients who have been subjected to FGM.
FGM was first made illegal in Britain under a 1985 law, which was extended in 2003 to make it an offence for British nationals or permanent residents to carry out FGM abroad or seek FGM abroad, even where it is legal.
The maximum penalty is 14 years in jail.
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