After his baccalaureate, he studied medicine in Burundi where after he finished, he worked at the Christian hospital of Lemera in South-Kivu DR Congo, he was shocked when he realized the difficulty of childbirth for the women in the rural milieu because these women are brought to the hospital riding on a donkey, after having bled out from their difficulty during childbirth in residence.
Others quite simply came to die in the hospital because they waited to long after laboring for hours unsuccessfully. The surviving patients left with serious genital lesions.

He went to France to study gynaecology, and returned to set up a clinic in Lemera, South Kivu in the east of the country.
In 1989, Dr. Mukwege settled at the Hospital of Lemera close to these women where he will install a service of gynaecology/obstetrics after training the support staff. This service became known in the area and beyond the borders of the country.
The hospital was destroyed in 1996, during the civil war. Almost as soon as a new clinic in Bukavu opened, it became obvious to Dr Mukwege there was a special need for a clinic that dealt with victims of sexual violence.

Working in Panzi Hospital in Bukavu, where he specializes in the treatment of women who have been gang-raped by Congolese militia, Mukwege has probably become the world's leading expert on how to repair the internal physical damage caused by gang rape.
He has treated 21,000 women during the Congo's 12-year war, some of them more than once, performing up to 10 surgeries a day during his 18-hour working days.This dedication and this commitment had earned him the nick name of “Angel of Bukavu.”

Mentioned for two consecutive years as a candidate for the Nobel Prize, Dr Mukwege is the laureate of the Olof Palme Prize, of the African of the Year by the Nigerian media group Daily Trust, and of the UN Human Rights Award—all awarded in 2008.