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Background: Access to safe, effective, affordable, and high-quality medications has been included in the Sustainable Development Goals (SDGs) of the United Nations as a crucial step towards attaining universal health coverage. Access to medicines is a fundamental human right. If medicines are accessible and affordable, they save lives by reducing mortality and morbidity associated with acute and chronic diseases. WHO recommends that all countries voluntarily reach the minimum target of 80% availability of medicines by 2025. The primary purpose of this research is to assess access to essential medicines in Juba County, South Sudan., Methods: This study was undertaken using the standard World Health Organization/Health Action International Organization (WHO/HAI) approach for surveying the prices, availability, and affordability of medicines. A survey was conducted in six payams of Juba County, South Sudan, and 55 health facilities were assessed., Results: Prices for generic medicines were better in faith-based health facilities with a median price ratio of 1.95. Private pharmacies and private clinics had MPRs of 4.64 and 4.32, respectively. Local prices were high compared to International referent prices. Availability of medicines was highest in the faith-based health facilities (65.5%) and slightly lower in private pharmacies (55.4%), private clinics (57.7%) and public (50.4%) sectors. Most of the surveyed medicines were unaffordable. The medicines needed to treat non-communicable diseases cost up to 33.7-day wages for one full course of treatment., Conclusions: In South Sudan, medicines are poorly available in all sectors. Medicines are affordable in the public sector but Most medicines are unaffordable in private pharmacies, private clinics and faith-based health facilities. Poor medicines availability in the public sector contributes to the overall unaffordability of medicines in all the other sectors., (© 2023. The Author(s).)