In a memo to Secretary of State John Kerry, the president said "it is important to the national interest" to provide the assistance to meet "unexpected urgent refugee and migration needs resulting from the crisis" in South Sudan, Xinhua reported.
The money, the president said, would fund international, governmental and non-governmental organisations as well as cover expenses of the State Department's Bureau of Population, Refugees and Migration in the region.
"Months of conflict between the government of South Sudan and rebel forces have exacted a terrible toll on the people of South Sudan," White House National Security Council spokeswoman Caitlin Hayden said in a statement.
"More than 1.3 million people have been displaced, and the country is now at risk of famine unless humanitarian agencies are able to scale up relief efforts and access those in need."
A cease-fire agreement reached between South Sudan's warring sides on May 9 has failed again to stem the conflict, which broke out in mid-December last year.
Tens of thousands of people have been killed since, and more than 300,000 people have fled to neighboring countries.
Hayden said the 50 million dollars in aid announced by Obama would be part of a 300-million-dollars assistance the US delegation would unveil on Tuesday at a pledging conference in Oslo, Norway, bringing the total US humanitarian aid since the start of the conflict in South Sudan to about 434 million dollars.