Authorities say 554 people have arrived since the start of the month.
They are among nearly 100,000 South Sudanese refugees in the DRC's Haut Uele and Ituri provinces, according to the UNHCR.
Refugees are flooding into the remote northeast of the Democratic Republic of Congo from South Sudan as a September 2018 peace deal hangs in the balance.
The refugees, sheltering in the town of Aru in Ituri province, fled fighting along the border between South Sudan and Uganda, the DRC's neighbour to the east.
Fighting has persisted between government forces and rebels of the National Salvation Front who reject the peace accord between South Sudan's President Salva Kiir and his arch-foe Riek Machar.
"Among the refugees... there are a lot of widows, as well as unaccompanied children," said Andreas Kirchhof, spokesman of the UN refugee agency UNHCR in the DRC.