The hospital was opened in 1952 by American missionaries.
Operations were disrupted during the Burundian Civil War.
In 2006 the missionaries returned, and called on the surgeon Dr. Elysée Nahimana to manage the hospital, which at first had only six nurses.
In May 2011 eight doctors from Stichting Interplast Holland came to Kibimba Hospital at the invitation of Izere, an association of the Burundi diaspora in Holland. They operated for five days on patients suffering from deformities such as harelips or scarring from burns.
They were not able to operate on all the people who had travelled to the hospital in the hope of having an operation, and promised to return later to continue their work.[4]
As of 2012 the 198-bed hospital was treating patients from remote area such as Makamba and Cankuzo, who could not receive surgery at home and were drawn by the hospital's reputation for good quality care.
Many of the patients were poor and could not afford to pay their bills.
The hospital in 2017 had recently developed its surgical department.
As of April 2019 the hospital had 50 nurses and five doctors, including a specialist.
There was a maternity block for 60 women and a pediatric block.
The operating room and sterilization room had been rehabilitated.
The hospital contacted the "MPR Development" program in 2017 for help in creating a physiotherapy department.
An existing building was converted for this purpose, and equipment was installed between October 2019 and June 2020 at a cost of 15,677 euros.
In March 2024 Evariste Ndayishimiye, President of Burundi, visited the hospital and gave out food assistance to the poorest patients.
He also visited the site of a three-storey extension to the hospital that was being built to accommodate pregnant women and sick children under 5 years old.
