Community-wide distribution of azithromycin, otherwise known as mass drug administration (MDA), is a component of the World Health Organization-endorsed SAFE strategy for the elimination of trachoma as a public health problem. In the Republic of South Sudan, 2.9 million people are known to live in areas that are known to require interventions and warrant MDA. This study estimated the total costs and cost per person treated during MDA in two counties, Kapoeta North and Kapoeta East, in South Sudan. MDA was conducted in Kapoeta North and Kapoeta East counties from October 2020 to January 2021. Following training and community sensitization, a core team, consisting of a height measurer, a drug dispenser, and a data recorder, delivered the intervention. A detailed costing database was developed in Microsoft Excel. An ingredients approach was used to capture all financial and economic costs incurred from a payer perspective. Primary outcomes included the total cost of MDA in each county and the cost per person treated in each county. In Kapoeta North, 58,226 people were treated at a financial cost of $71,350 USD. This corresponds to a unit cost of $1.22 per person treated. The total economic cost of the intervention was $99,036, at a unit cost of $1.70 per person treated. In Kapoeta East, 156,092 people were treated at a total financial cost of $168,404. This corresponds to a unit cost of $1.08 per person treated. The total economic cost of the intervention was $243,205, at a unit cost of $1.56 per person treated. The study highlights the cost variation for MDA implementation across two counties of South Sudan. As the South Sudan trachoma program expands, this information will be valuable for program planning.