Some of the money will come from the US Emergency Refugee and Migration Assistance Fund and will be used to support the United Nations and other refugee organisations.
The White House says the UN and its partners are urgently assisting the more than 300,000 refugees that have crossed into Ethiopia, Kenya, Sudan and Uganda, as well as internally-displaced persons in South Sudan.
Obama authorised the emergency funding ahead of a South Sudan pledging conference scheduled for today in Oslo, Norway.