The study investigated and sought to establish the relationship between internal control systems and financial performance in Institutions of higher learning. Internal controls were looked at from the perspective of Control Environment, Internal Audit and Control Activities whereas Financial performance focused on Liquidity, Accountability and Reporting as the measures of Financial performance. The Researcher set out to establish the causes of persistent poor financial performance from the perspective of internal controls. The study found that management of the institutions is always committed to the control systems, actively participates in monitoring and supervision of the activities, that the internal audit departments are not usually efficient, are usually understaffed, don¿t conduct regular audit activities and don¿t produce regular audit reports although the few reports produced acted upon The Study concluded that internal control systems in Institutions of higher learning normally do function although with hiccups and that there is a significant relationship between internal control systems and financial performance in an Institution of higher learning.