Internal Control Systems play an essential role in every organization as it assists in the realization of their financial performance goals. Internal controls minimize risks and protect assets, ensure accuracy of records, promote operational efficiency, and encourage adherence to policies, rules, regulations, and laws. The central aim of the research was to reconnoitrer the Effect of Internal Control Systems on the Financial Performance of Commercial Banks in Rwanda. The study was guided by the following goals and purposes; to investigate the relationship between the internal control environment on the Financial Performance of Commercial Banks in Rwanda and to establish the effect of risk management on the Financial Performance of Commercial Banks in Rwanda. Most Commercial Banks in Rwanda in recent years performed poorly due to weak internal control systems, record keeping, financial reporting, and regulatory compliance. The study adopted System Theory and agency theory. The study adopted a descriptive research design using both quantitative and qualitative approaches. The study adopted a target population of 96 and multi-level random sampling of 38 Senior Managers in various categories.