The general objective of the study was to determine the effect of the internal audit function in the financial performance of financial institutions in South Sudan. The study had three specific objectives in looking at the internal audit function; the role of the internal auditor’s competencies to the financial performance, the effect of the internal audit independence and the role of the audit committees to the financial performance of the financial institutions. The study adopted a descriptive research design and used research questions to collect data from the respondents. The sample population was 104 people covering the internal audit departments, finance staff, the audit committees and the risk departments of the 11 financial institutions in South Sudan. Data on the financial performance measure was collected from the bank’s supervisory reports in the Central Bank of South Sudan website. The study used quantitative and qualitative techniques to analyze the results obtained from the data collected. The data collected was coded with the use of Statistical Package for Social Sciences (SPSS version 24) and Microsoft excel. The data was interpreted using frequencies, percentages, mean, and standard deviation and presented using tables and figures. Multiple regression was used to establish the relationship between the variables. Correlation analysis was used to establish the significance of the relationship of the variables. The study covered a five-year period 2017-2021. From the findings, the study concludes internal auditor’s competencies in educational, professional and technical skills contribute to the financial performance of the company. Internal audit is effective in executing its responsibilities with qualified staff who ensure control lapses are timely reported, and corrective action is taken to prevent losses and wastage in the organization. The study emphasizes on the outcomes of the internal audit independence in reporting as it ensures there is objectivity in reporting control issues noted during their reviews. The role of the audit committees in providing an oversight role to the internal audit function is noted to be critical as it ensures the IAF is effective in the organization. From the study, it is noted that three variables have a significant positive relationship with financial performance of the 11 financial institutions in South Sudan. The study recommends that the internal auditors should be properly resourced and continuous training done in workshops and seminars to improve their skills and update themselves with new technology to improve on their audit reviews. The study further recommends autonomy be given to the IAF in order to promote their independence and objectivity in reporting. The study noted the audit committees have an oversight role on the IAF hence there is a need to ensure the members of the AC are independent and possess the financial skills to understand the financial estimates and assumptions.

A Research Dissertation Submitted to the School of Business Administration in Partial Fulfillment of the Requirements for the Degree of Masters in Business Administration (MBA) of Nkumba University