Indirect effects of the COVID-19 pandemic on communities in fragile and conflict-affected settings may be severe due to reduced access and use of healthcare, as happened during the 2015 Ebola Virus Disease outbreak. Achieving a balance between short-term emergency response and addressing long-term health needs is particularly challenging in fragile and conflict-affected settings such as South Sudan, given the already significant barriers to accessing healthcare for the population. This study sought to characterise the effect of COVID-19 on healthcare access and South Sudan’s healthcare response.