The role played by small and medium enterprises in the growth and development of economies is critical. Understanding how firms improve their performance to achieve competitiveness should, therefore, concern countries keen on economic growth. However, small and medium enterprises face growth challenges because they operate simultaneously in the global and local markets, making innovation imperative. This study investigated the effect of cost reduction capabilities and organisational structure capabilities on the competitive advantage among Medium-Sized Enterprises (MSEs) in Juba, South Sudan. The study was guided by the resource-based theory and dynamic capability theory. The target population constituted 491 MSEs operating in Juba, South Sudan. Yamane formula was used to calculate the sample size of 246 MSEs, which was selected using stratified and random sampling techniques. Questionnaires were used for data collection, and the data was analysed using descriptive statistics and multiple linear regression. The results indicated a positive and statistical significance between organisational structure (β = 0.582, t = 9.569, p < 0.05) and the competitive advantage among MSEs in Juba, South Sudan. The study concluded that a formal organisational structure significantly affected the competitive advantage of MSEs. The study recommended that management should strengthen their organisational structure to facilitate the development and enhancement of leadership capabilities.