Provision of quality secondary education is important in generating the opportunities and benefits of social and economic development. Among the strategies adopted for expanding access to secondary school education in Kenya, is subsidizing secondary education. The purpose of this study was to examine the administrative challenges facing public secondary schools in the wake of subsidized secondary education in Nakuru Municipality Kenya. The study adopted the descriptive survey design and the sample size was identified and selected using purposive sampling technique. The study used a study sample size of 24 schools from which 144 respondents were interviewed. Data was collected by use of questionnaires and an interview schedule. Data collected was then analysed with the aid of the Statistical Package for Social Sciences version 17 for computation of descriptive statistics (frequencies and percentages), and non parametric tests (chi-square tests). After data analysis, the results were presented in the form of charts and tables for ease of interpretation. The findings revealed that teacher shortage, leadership style adopted by head teachers and teacher remuneration presented as challenges affecting administration of public secondary schools in advent of subsidized education in Nakuru Municipality; The type of leadership style as a challenge was experienced by head teachers to a small extent; The strategies suggested by administrators of public secondary schools to mitigate challenges in the advent of subsidized education in Nakuru Municipality were included prompt disbursement of funds to schools; teacher motivation should be enhanced through increased remuneration, promotions and better working conditions; government to provide adequate funds to schools and employ enough teaching staff; increase teaching staff; laboratory to be well equipped; parents need to sensitized on their role in the teaching and learning process; additional resources to cater for increased pupils in schools; train more teachers; improve infrastructure; schools in hardship areas to be given more money. The study recommended that the Government of Kenya (Ministry of Education) should consider: mobilizing resources to increase the allocation disbursed to schools; reviewing its policy on funds disbursement to ensure promptness in disbursement; organizing more resources to support financial education and management training and workshops, new technology usage computers and internet training, review on government policies on money disbursement to schools refresher courses regularly to improve skills for the school head teachers and all persons involved in the school management; employ enough teaching staff and enhance teacher motivation through increased remuneration, promotions and better working conditions. The School management teams should consider organizing regular meetings with parents to encourage their support to school projects and programmes. The study findings could be useful for the enhancement of the regulatory mechanisms geared towards enhancement of quality management practices in respect to subsidized secondary education programme in Kenya.