The study examines the effect of internal control on financial management of selected universities in Nigeria. The methodology of this is study is based on the survey research approach. It involves the distribution of one hundred and fifty (150) copies of questionnaire to some selected universities in the South West of Nigeria. These universities were selected using purposive sampling technique. The data obtained from the questionnaire were analysed using both descriptive statistic and inferential statistic such as frequency tables, percentages and chi-square analysis. The result of the analysis shows that there was significant relationship between internal control and prudent management of the resources, this is because the chi-square value calculated (i.e. 128.000) was greater than the chi-square value tabulated (i.e. 9.488). Therefore, based on this result the study recommends that management should develop stronger policies that will encourage a strong and reliable internal control system so as to encourage the prudent management resources of the selected universities.