Research has shown that financial resources do not always impact significantly on academic performance. This would suggest that financial resources are not a major factor in determining academic performance in secondary schools. The purpose of this research was to find out whether factors like financial leakage, governance, accounting controls and auditing, allocation of resources to teaching and learning and ownership structures can be used to establish the link between resources and academic performance. The population of this study comprised of all the 336 registered secondary schools in Nakuru County of which 33 were randomly sampled. The County was stratified into administrative Districts and the schools into public and private schools. Pre-tested Questionnaires and observation guides were used to collect information from the respondents. Cronbach‘s alpha was used to establish the reliability and validity of the data collected. The data collected was collated, cleaned, coded and entered for analysis using Kendall‘s, Pearson‘s and Spearman‘s correlation coefficient, goodness of fit test, simple linear and multiple regression tests, to establish the links among the variables. The findings of this study suggest that the income of the school and books provided to students, accounting controls and governance are major factors in determining the performance of schools in KCSE. Physical facilities, Heads score, Bursar‘s score, perceived provision of resources, perceived corruption levels and ownership structures were found not to be significant in determining academic performance. Prices at which schools bought goods in the market were not influenced by the ownership structures. Leakage of resources was negatively related to performance in KCSE. The study found the need to develop an accounting system to enhance governance, accounting controls and auditing, and capture information to provide traceable audit trails.