 top five poorest countries in Africa. The top three 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.