Dr Dhanuson Dharmasena, 31, from Whittington Hospital, north London, and Hasan Mohamed, 40, who is not a medic, face the first charges brought under the Female Genital Mutilation Act (2003).
It is alleged the doctor carried out the procedure on a woman who had given birth in November 2012. He is accused of repairing FGM that had previously been performed on the patient and Mohamed allegedly encouraged and helped.
The defendants' lawyers indicated to Westminster Magistrates' Court that the pair would plead not guilty. The doctor, of Ilford, Essex and Mohamed, whose address was not read in court, were granted unconditional bail.
They will appear at Southwark Crown Court on May 2.