BACKGROUND: People in humanitarian emergencies are likely to experience excess mortality but information on the causes of death is often unreliable or non-existent. This study aimed to provide evidence on the causes of death among children younger than 5 years in camps for internally displaced people in southern Somalia, during periods of protracted displacement and emergency influx amid the 2017 drought and health emergency. METHODS: We did a prospective, cohort study in 25 camps in the Afgooye corridor, on the outskirts of Mogadishu, Somalia. All internally displaced children aged 6-59 months were included and followed up with monthly household visits by community health workers. Nutrition, health, and vaccination status were ascertained and verbal autopsy interviews were done with the caregivers of deceased children. We calculated death rates in these children and used verbal autopsy to establish the cause-specific mortality fraction (CSMF). Bayesian InterVA software was used to assign likely causes to each death. FINDINGS: Between March, 2016, and March, 2018, 3898 children were followed up. 153 deaths were recorded during 34 746 person-months of observation. The death rate among children younger than 5 years exceeded emergency thresholds (>2 deaths per 10 000 children per day), reaching a peak of seven deaths per 10 000 children per day during the emergency influx. Verbal autopsy data were gathered for 80% of deaths, and the CSMF for the three leading causes of death were diarrhoeal diseases (25·9%), measles (17·8%), and severe malnutrition (8·8%). Coverage of measles vaccination during the first 3 months of the emergency was 42% and the CSMF for measles doubled during the influx. During protracted displacement, symptoms that could be attributable to HIV/AIDS related deaths accounted for 1·6% of the CSMF. INTERPRETATION: It is feasible to establish a health and nutrition surveillance system that ascertains causes of death, using verbal autopsy, in this humanitarian context. These data can inform policy, response planning, and priority setting. The high mortality rate from infectious diseases and malnutrition among children younger than 5 years suggests the need for strengthening a range of public health interventions, including vaccination and provision of water, sanitation, and hygiene. FUNDING: UK Department of International Development.