Female genital mutilation (FGM) includes procedures involving the partial or total removal of the external female genitals for non-therapeutic reasons. They can have negative psychosexual and health consequences that need specific care. In this paper, we review some key knowledge gaps in the clinical care of women with FGM, focusing on obstetric outcomes, surgical interventions (defibulation and clitoral reconstruction), and the skills and training of healthcare professionals involved in the prevention and management of FGM. We identify research priorities to improve the evidence necessary to establish guidelines for the best multidisciplinary care, communication, and prevention, and to improve health-promotion measures for women with FGM.