The novel coronavirus disease (COVID-19) was first reported in Sudan on 13 March 2020. Since then, Sudan has experienced one of the highest rates of COVID-19 spread and fatalities in Africa. One year later, as per 22 March 2021, Sudan had registered 29,661 confirmed cases and 2,028 deaths with a case fatality rate (CFR) of 6.8 %. By 12 December 2020, of the 18 states in Sudan, South Kordofan had the fifth highest CFR of 17.4 %, only surpassed by the other conflict affected North (57.5 %), Central (50.0 %) and East (31.8 %) Darfur States. By late March 2021, just three months from December 2020, the number of cases in South Kordofan increased by 100 %, but with a significant decline in the CFR from 17.4 to 8.5 %. South Kordofan is home to over 200,000 poor and displaced people from years of destructive civil unrests. To date, several localities such as the Nubba mountains region remain under rebel control and are not accessible. South Kordofan State Ministry of Health in collaboration with the federal government and non-governmental organizations set up four isolation centres with 40 total bed capacity, but with only two mechanical ventilators and no testing centre. There is still need for further multi-sectoral coalition and equitable allocation of resources to strengthen the health systems of rural and conflict affected regions. This article aims at providing insight into the current state of COVID-19 in South Kordofan amidst the second wave to address the dearth of COVID-19 information in rural and conflict affected regions.