"Our humanitarian experts in the crisis areas have alerted me that the situation is deteriorating fast and the needs are growing," Kristalina Georgieva, the European aid commissioner, said in a statement. "It is vital to scale up our immediate response in the border areas."
South Sudan gained independence last year under the terms of a 2005 peace deal that ended one of the bloodiest wars in modern history. Ethnic fighting and outstanding issues like border demarcation are threatening the fragile peace, however.
The European Commission said the humanitarian situation in South Sudan had "deteriorated drastically" this year. In Sudan, meanwhile, conflicts in border states and ongoing violence in Darfur are exacerbating the situation.
Both parties to the conflict met this week in the Ethiopian capital in an effort to hammer out their differences.
South Sudan's economy is in shambles because of a January decision to halt oil production in retaliation for alleged Sudanese pilfering. Sudan, meanwhile, has seen inflation hit the double digits, sparking protests in Khartoum.
The European aid contribution brings its total for the year to $127 million.