The idea for establishing the Ghana Cleft Foundation originated in 2005 from discussions among members of the Komfo Anokye Teaching Hospital Cleft Clinic. These discussions were informed by the firsthand experiences of the hardships faced by families of children born with cleft lip and palate.  The Cleft Clinic attracts patients from all parts of the country, majority of whom are from low income backgrounds. These families faced a great deal of prejudice from their communities which understood very little about cleft lip and palate and were largely treated as outcasts. Some mothers had been forced out of their homes for refusing to abandon their children. Most of the affected children that are seen come from very poor families who often find have difficulty with raising the needed funds for nutritional supplementation, transportation to the clinic and to pay for needed surgery.
It was clear that meeting the needs of cleft patients went beyond being attended to by a health professional. There was also the need to understand the causes and extent of cleft problem in Ghana, to assist in training cleft specialists to fund cleft research. This awakening inspired the desire to generate resources to help needy cleft patients.

Following a series of consultative meetings with a number of stakeholders a constitution was drawn up which eventually led to the incorporation of the Ghana Cleft Foundation in 2006 as a non-profit charitable organization. The Founding Board Members were drawn from volunteers representation a wide area of professional endeavour.