This study examined the reform Agenda and the educational policy in Kenya with regard to the secondary school sector in Eldoret municipality. The study was based on the social systems theory as advanced by Newstrom (1993). The research adopted an exploratory survey design. The target population was the principals in secondary schools, the student governing council, teachers and parents. The sample was selected using proportionate stratified random sampling and purposive sampling. Data was collected by use of questionnaires, interview schedules, and observation schedule. Descriptive statistics, (percentages, frequency distribution tables and graphic representations) were used in data analysis and interpretation of data. The significance of the study lies in the fact that reform agenda in education with regard to educational policy is aimed at creating equal opportunity for all learners in Kenya. The study findings revealed that the education opportunities at secondary school level are unevenly distributed, ranking of schools based on performance create discrimination. The admission criteria have created a rift rather than promote unity, and that affirmative action in the education sector has led to inequalities. The study concludes that, the government of Kenya needs to redirect some public resources for education from the wealthiest people to the poor population. Concludes that unless the regional differences are considered educational policies will always replicate social injustices.