In the face of the rising cost of secondary education, the concept of unit cost of secondary education is gaining great importance. This study analyzed Unit Cost of Day and Boarding secondary schools in Nandi County, Kenya. Specifically the study sought; to establish variable cost, to determine unit cost, to compare unit cost and government fees limits and to compare unit cost of Day and Boarding secondary schools. This study was guided by Cost Function derived from the Education Production Function theory. The study employed survey as a research strategy; targeted all the principals in 186 public secondary schools, It employed stratified random sampling and then systematic random sampling. A pilot study was used in determining the reliability where Pearson Product Moment Coefficient (r) of 0.807 was obtained. For Validity of the research tools, experienced team of supervisors carefully and critically examined the instruments. Data was analyzed using means, percentages and ttest. The findings revealed that, Variable cost for the period (2012-2015) in Day and Boarding schools was Ksh.1.2 billion and Ksh.1.7 billion respectively. It was found out that, average unit cost for the period 2012-2015 was Ksh. 22,263 and Ksh. 54,828 for Day and Boarding schools respectively. This study found out that, majority (70%) of the Boarding schools spent within the set government fees limit while majority (76%) of the Day schools in this study spent beyond the set limit; there was a significant difference in unit cost between Boarding and Day secondary schools. (t(121) = 31.516, p = 0.000); The findings of this study will generate ideas for better and more ingenious cost management. To manage unit cost of secondary education, there is need to; appreciate the concept of cost unit cost, improve effectiveness of school management, effectively utilize monetary resource and practice prudence in financial management.