Top 5 poorest countries in Africa. The top 3 poorest countries in Africa are in East Africa, a region which continues to be held back by problems such as institutional weakness, corruption, poor infrastructure, insecurity and a lack of human capital. 5. Central African Republic, GDP per capita, $492.08. 4. Madagascar, GDP per capita, $471.05. 3. Mozambique, GDP per capita, $448.05. 2. Somalia, GDP per capita, $438.03. 1. Burundi, GDP per capita, $239.