The U.N. Office for the Coordination of Humanitarian Affairs (UNOCHA) said in the latest episode of fighting in Fashoda County that started in mid-November, some 9,100 people had been displaced.
Of these, over 2,300 who had sought refuge in the Malakal Protection of Civilians site, an UNOCHA statement said.
"According to local responders at least 75% of the newly displaced are women and children, with many children separated from their caregivers," it said.
UNHCR said at least 3,000 had fled to neighbouring Sudan.
"Fleeing civilians are visibly traumatised and report killings, injuries, gender-based violence, abductions, extortion, looting and burning of properties. Many have lost their homes and been separated from their families," UNHCR said.
The latest bloodshed is a continuation of fighting that started in August in a village in Upper Nile and has since spread to other parts of the state and areas of Jonglei and Unity States, U.N refugee agency UNHCR said in a statement.
A peace agreement signed in September 2018, the latest in a series reached since the conflict began in late 2013, is largely holding. South Sudan's civil war, often fought along ethnic lines, is estimated to have claimed close to 400,000 lives.