What is already known about this topic? As of March 2021, African countries have reported fewer COVID-19 cases than have countries in other regions. The extent to which this is due to surveillance limitations is unknown. What is added by this report? Policy, funding, and strategy changes in South Sudan influenced the number of SARS CoV-2 tests performed and the populations tested. Underreporting of testing rates and detected cases, including a February 2021 COVID-19 surge, might have occurred after policy changes led to an increase in travel screening of asymptomatic persons with no known contact with a positive case and a decrease in testing of suspected cases