In June 2020, a door-to-door household survey was conducted in Mvolo County, an onchocerciasis endemic area in South Sudan. A total of 2,357 households containing 15,699 individuals agreed to participate in the study. Of these, 5,046 (32.1%, 95%CI: 31.4-32.9%) had skin itching and 445 (2.8%, 95% CI: 2.6-3.1%) were blind. An epilepsy screening questionnaire identified 813 (5.1%) persons suspected to have epilepsy. Of them, 804 (98.9%) were seen by a medical doctor and in 798 (98.1%) the diagnosis of epilepsy was confirmed. The overall epilepsy prevalence was 50.8/1000 (95% CI: 47.6-54.4/1000) and prevalence of nodding syndrome was 22.4/1000 (95% CI: 20.1-24.9/1000). Younger age, being male, skin itching, blindness and living in a village close to the Naam river were risk factors for epilepsy. The annual incidence of epilepsy was 82.8/100,000 (95% CI: 44.1-141.6/100,000). In conclusion, a high prevalence and incidence of epilepsy was observed in Mvolo, South Sudan. Strengthening the onchocerciasis elimination programme is urgently needed to prevent epilepsy in this region.