research objective was to investigate the effect of the internal control systems on the financial performance in the Nairobi Stock Exchange (NSE) listed banks in Kenya. The study posits that risk assessment and information and communication have a weak significant effect while the monitoring, control environment and the control activities have the weakest influence on ROA and ROE in the NSE listed banks in Kenya. The study used a descriptive research design and a case study to analyse the impact of the variables on financial performance using Likert collected responses. The correlation results established that monitoring, information and communication, control environment, risk assessment and control activities have positively influenced the performance as they all had positive values. The R squared values of .0664 for ROA and 0.742 for ROE showed a good fit. The F statistic was also significant showing that the independent variables were significantly different and that each could contribute differently to the financial performance of NSE listed banks. The internal controls: risk assessment and the controlled environment have features in them that are essential in establishing any corrupt activities occurring within the banks. To enhance performance and mitigate adverse corporate governance issues management requires that the banks must have strong internal control systems that have been put in place. To facilitate faster delivery of audit activities which includes the processes of detecting and preventing of frauds and/or non-compliance with public expenditure, the Nairobi Stock Exchange listed banks should provide a conducive control environment that enables the use of cutting-edge control activities such as ICT technology to support auditing functions, accounting packages among other which will promote continuous training and develop organizational.