"A group of unidentified armed men broke into (the) MSF office and compound, looting the organization and staff's properties, burning down a tent full of equipment and destroying most of the vehicles and communication devices," the medical charity said in a statement.
"The attack has forced MSF to suspend the majority of its medical support to the host communities and the refugee population."
MSF head of mission Samuel Theodore said the team would continue to treat those with the most critical medical conditions.
"However, as the safety of healthcare personnel and facilities cannot be guaranteed, we have no other choice but to suspend the rest of our activities, which will leave 88,000 people with limited access to much needed medical services."
The violence occurred after locals protested a lack of job opportunities, accusing humanitarian organizations of hiring from outside the county, UNHCR said.
Aid workers have frequently been targeted during South Sudan's four-year-long civil war, with 100 killed since the outbreak of fighting in December 2013, according to the UN.
Thousands of aid workers work in the country which is suffering one of the worst humanitarian crises in the world, with four million displaced and seven million -- more than half the population -- requiring food aid in 2018, according to the UN.
