The UNICEF says Malaria cases have continued to rise in the Greater Bahr Al Ghazal region, and Unity state.
It says it will screen about 35, 000 children under 5 years for the disease.
In a statement, UNICEF says it is working with MSF and WHO to scale up response in the Protection of Civilian’s Site in Bentiu.
It says they are carrying out “presumptive treatment” at household level on children less than 5 years with fever.
The UNICEF and the WHO have also initiated a joint nutrition plan to reduce malnutrition among children.
“Malnutrition in South Sudan is a chronic problem, and an acute emergency,” the statement read.