Manufacturing companies in Nigeria has witnessed poor financial performance, subsequent failure and liquidation which can be traced to weak internal control system, internal fraud, and non-compliance with corporate governance standard, lack of transparency, creative accounting and insider trading. The financial performance of manufacturing companies has been called to question on several occasions. The study examined the effect of internal control system on financial performance of manufacturing companies listed in Nigeria. The study employed ex-post facto research design, a target population of forty-three (43) manufacturing companies quoted on Nigerian Stock Exchange was used and a sample of fifteen (15) companies was selected from the population. The data was gathered from audited financial reports of the sample manufacturing firms for a period of ten (10) years. The study employed descriptive method of analysis to describe the data while inferential statistics such as multiple linear regression technique was used to test the hypotheses using Stata software. Inferences were made at 10% level of significance. The study showed that Risk management has significant and positive effect on financial performance of manufacturing companies listed in Nigeria giving the F-statistics value of 7.212 with probability value of 0.000 and Adjusted r2 of 0.151. Hence the null hypothesis of no significant effect is rejected. Board independence have statistical impact on financial performance with F-statistics value of 5.441 with probability value of 0.000 and Adjusted r2 of 0.113. Hence the null hypothesis of no significant effect is rejected. From the findings of the study, the study concluded that manufacturing companies that had invested on effective internal control systems have more improved financial performance as compared to those with a weak internal control system. The following recommendations were made based on the outcome of the study: Management should develop a mechanism to incorporate relevant feedback from the various stakeholders into their internal control system and Board of Directors of manufacturing firms should ensure that the internal control systems recommended by both internal and external auditors are periodically monitored and evaluated.