With the deterioration of the political context in Burundi since April 2015 more than 140,000 refugees have arrived in Tanzania. The refugees are hosted in three camps in Kigoma region, together with 83,000 Congolese refugees living in Nyarugusu camp for almost 20 years. The initial influx of Burundi refugees coincided with a cholera outbreak in Kigoma region, which triggered an immediate MSF emergency response in May 2015. This rapidly shifted with the movement of refugees from the lake shore of Tanganyika to the Nyarugusu camp. Despite the initial focus on cholera, due to precarious living conditions of refugees and problematic access to health care, MSF started to provide limited humanitarian assistance in Nyarugusu camp since July 2015. As UNHCR with its implementing actors were established in the camp before MSF arrival and the Burundi refugees were supposed to be quickly relocated to other camps, MSF envisaged only a short presence with direct support for the most urgent gaps while lobbying to other actors for rapidly scaling up their humanitarian assistance. Due to UNHCR failure to relocate the refugees, inadequate response by other actors and high mortality rates in children during the malaria peak, MSF stayed in Nyarugusu and reinforced its direct support, especially in secondary health care. In Nduta camp, based on lessons learned from Nyarugusu, MSF positioned itself as a main emergency actor with an involvement in medical, water, sanitation and hygiene (WASH) and shelter. As the sole health care provider in the camp, MSF was progressively scaling up its activities, providing a wide range of services. Currently, the humanitarian situation has been stabilised, entering into a post-emergency phase. However, in absence of a solid organisation to take over the medical activities MSF remains the main health actor in Nduta during the post-emergency phase. In light of a planned handover from the emergency cell to the regular cell, an evaluation was commissioned to capitalize on the lessons learned from the emergency phase of the intervention.