Since independence in 2011 the Republic of South Sudan has witnessed growth in the financial systems and the overall economy. This has led to growth in the number of the financial institutions in the country. There is however minimal research on their overall performance. Hence the current research sought to determine the effect of ownership structure, bank stability and the financial performance of commercial banks in South Sudan. The population for the study was all the 29 commercial banks in South Sudan. Secondary data was collected for the period 2012-2017 from audited annual financial reports of individual banks and from the Central Bank of South Sudan reports while primary data was collected by use of a semi-structured questionnaire. The research utilized both descriptive and inferential statistical methods in the analysis. The statistical tests to be utilized in the study included t-tests, f-test, regression models and ANOVA models. The results of the study indicated there was a statistically significant moderating effect of ownership structure on the financial performance of commercial banks in South Sudan. The study recommends that the government should adopt better measures to safeguard public owned commercial banks to improve their efficiency and performance.