Internal control systems play a vital role in achieving the objectives of an organization. This study investigated the relationship between internal control system and financial performance of tertiary institutions in Nigeria using four tertiary institutions in South West, Nigeria. Data was collected through primary source using questionnaires. The method of data analysis was Canonical Analysis. Findings revealed that the components of internal control system are not properly situated by the management and hence internal control systems of tertiary institutions are not adequate. The study therefore recommends that for there to be an effective internal control system, there should be a functional internal audit unit/ department and it should report to the governing council or the highest authority in the institution and recruitment of staff in that unit should be exclusive to accountants.