The International Development Committee (IDC) said the money would help some of Africa's "most vulnerable" people.
The cash will be split evenly between Action Aid - who are working with refugees from Burundi - and Medair, who are working in South Sudan.
Both charities will use the money to offer water, healthcare and emergency shelters.
The ongoing constitutional crisis in Burundi, where there is violent conflict between supporters of the government and opposition, has resulted in thousands of people seeking refuge in neighbouring countries.
South Sudan gained independence from Sudan in July 2011 and, according to the IDC, continues to be "besieged by conflict".
IDC Chairman Phil Gawne said: "Through these donations the Isle of Man is helping to provide vital assistance to a large number of vulnerable displaced people in areas overwhelmed by conflict."
10.4m population
50 years - life expectancy for a man
2nd poorest country in the world
85% are Hutu, 14% Tutsi
300,000 died in civil war
The Isle of Man has given £50,000 to charities helping refugees from Burundi and South Sudan.