On 3 March 2020, the Ministry of Health of South Sudan reported two presumptive positive cases of yellow fever in Kajo Keni county, Central Equatoria State, South Sudan. Both the cases were subsequently confirmed positive by plaque reduction neutralization testing (PRNT) at the regional reference laboratory, Uganda Viral Research Institute (UVRI) on 28 March.

The cases were identified through a cross-border rapid response team investigation mounted in response to the recently declared outbreak in bordering Moyo district, Uganda. During the investigation, the team collected 41 blood samples from five villages which were in close proximity to the bordering Moyo district, Uganda. Of the 41 individuals whose samples were collected, nine (22%) had history of fever, but none had history of jaundice. The individuals represented a spectrum of occupations typical for the area (farming, forestry, homemaker, soldier). Most of the individuals investigated were between 20-45 years of age, and 18 (44%) of these individuals were female.

In addition, a rapid entomology survey in the villages found evidence of multiple mosquito breeding sites and abundant Aedes species mosquitos (e.g. Aegypti , Albopictus, Simpsoni).

As of 28 March 2020, these are the only two cases (no deaths) that have been confirmed from Kajo Keji county.

South Sudan has experienced several yellow fever outbreaks in the past. The last outbreak was declared on 29 November 2018, in Sakure payam, Nzara County, Gbudue State when three laboratory confirmed cases with no associated deaths was reported. To respond to the outbreak, a targeted reactive vaccination campaign was mounted in the affected area. Prior to this outbreak, in May 2003, a total of 178 cases with 27 deaths were reported in Imatong region, Torit Country, South Sudan. A reactive vaccination campaign was mounted to respond to the outbreak in 2003.