About 8,000 young girls are circumcised every day in Africa and the Middle East, and the Desert Flower Medical Center, located in a Berlin hospital, will offer reconstructive surgery and psychological help to those among the 50,000 girls and women in Germany who need it.
The center is a pilot for others planned in Europe, Africa and Asia.
Dirie's genitals were mutilated as a Somali nomads' daughter at about age four, a fate she recalled in her bestselling autobiography "Desert Flower", which was turned into a 2009 movie.
"Female genital mutilation has nothing to do with religion, culture or tradition. It is a crime against innocent girls" that must be punished, Dirie, the 48-year-old patron of the center, was quoted as telling Berlin daily the Tagesspiegel.
Female genital mutilation, or female circumcision, involves removing the external genitalia of young girls with the aim of ensuring their chastity as women.
The painful and sometimes fatal operation is usually carried out on girls between infancy and age 15. It can cause infections and, later, infertility and childbirth complications.
The UN World Health Organization says about 150 million girls and women worldwide are living with the consequences of what is known as FGM.
The Berlin medical center, located in the Waldfriede Hospital, will treat about 50 to 100 women a year, its chief surgeon Roland Scherer told AFP. Two patients this week will be women from Djibouti and Ethiopia.