The Fistula Foundation was founded as American Friends Foundation for Childbirth Injuries (AFFCI) in 2000 by Richard Haas and his daughter Shaleece. Mr. Haas served as a teacher in the Peace Corps in Ethiopia from 1967 to 1969, prompting him to return with his daughter to visit the East African country in 1999. The Haases visited the Fistula Hospital and were moved by the oasis of healing created by Dr. Catherine Hamlin and her late husband, Dr. Reginald Hamlin. They returned to California and established a US-based non-profit dedicated to supporting the treatment and prevention activities of the Fistula Hospital.

In 2003, a highly praised New York Times Op-Ed by Pulitzer Prize winning author, Nicholas Kristof, lauded the work of Dr. Hamlin and raised awareness of and funding for the hospital. In January 2004, the Oprah Winfrey Show invited Dr. Hamlin to speak about the plight of fistula patients in Ethiopia. In the first six weeks after her appearance on the show, over 6,000 donors contributed $1.3 million through the Fistula Foundation to Dr. Hamlin's cause. That spring, the Foundation changed its name to the Fistula Foundation to more succinctly describe the organization’s mission.

New York Times Writer, Nicholas Kristof, in June 2005 wrote another inspiring article about the Hospital, and in December 2005, the Oprah Winfrey Show aired another show about the Hospital, this time featuring Ms. Winfrey’s visit to the Hospital, titled "Oprah goes to Ethiopia". In summer 2005, the Foundation Board elected Ethiopian-American, Mr. Kassahun Kebede, as Chair of the Board and hired its first full-time Executive Director, Kate Grant.

In 2006, the Foundation earned the Better Business Bureau Seal for meeting all twenty of the Better Business Bureau Standards for Charity Accountability. In that same year, the Foundation also earned a 4-Star Rating from the charity rating service "Charity Navigator" and published its first Annual Report. Following that in 2007, the Foundation achieved another 4-Star Rating, which only 15% of charities have received in two consecutive years.

In 2006 and 2007, the Fistula Foundation furthered its mission by funding, among other things:

• The construction, building and furnishing costs for the new Fistula Hospital in Harrar, Ethiopia, serving fistula victims in an underserved region and providing emergency obstetric care to women at high risk of obstructed labor
• Medications and medical supplies required for fistula care at the Hamlin Fistula Hospital in Addis Ababa
• The building of Nurses Quarters near the Bahir Dar Fistula Hospital and maternal health unit upgrade
• Operating Support of the Hamlin Fistula Hospital to help fund life-restoring surgery for hundreds of patients
• The construction, building and furnishing costs for Nurses Quarters near the Harrar Fistula Hospital
• The construction, building and furnishing costs for the Nurses Quarters near the Yirgalem Fistula Hospital and water services upgrade
• Advanced Medical training for Fistula Hospital Senior Surgeon
• Medical conference for Addis Ababa Hospital Senior Staff
• Advanced Medical training for Fistula Hospital Senior Surgeon
• Computers and Software to help Hospital streamline its financial system
• Funding for the new Midwifery School
• 4 Wheel Drive Vehicles for use at the Hospital and the Midwifery College
• Incinerator for the Bahir Dar Fistula Hospital

Today, the Fistula Foundation continues to raise awareness and money for Hamlin Fistula Hospital's fistula repair, prevention, and education programs throughout Ethiopia.