The purpose of this study was to establish the challenges that confront principals of secondary schools in Nyamira County in Kenya. The study adopted a descriptive survey and questionnaires were employed to collect data. The study sample consisted of 87 principals purposively selected from schools in the County. The quantitative data from questionnaires was analysed with the aid of SPSS (statistical package for social science). The study established that principals faced serious challenges which included interference from sponsors, inadequate funds, inadequate resources and lack of qualified teachers among others. The study also identified the following as serious issues: teenage pregnancy, bullying, alcohol and drugs, violence and truancy among others. Such challenges and issues negatively impacted on the schools’ entire life including examination performances.