Students' participation in decision making on disciplinary matters plays an important role in influencing discipline in secondary school. However, students' perception determines the level of participation. The purpose of the study was to investigate the perception of secondary school students in Eldoret East, Uasin-Gishu County, on their participation in decision making, and its influence on discipline. The study was guided by the following objectives; to determine the perception of secondary school students on their participation in decision making and discipline, to investigate students' involvement in decision making in secondary schools, to establish the constraints to students’ participation in decision making in secondary schools, and to establish strategies used to enhance students' participation in decision making in secondary schools. This study used a mixed approach, using both qualitative and quantitative methods. The research instruments were questionnaires and interview schedules. The study sample comprised 369 form two students. The study used stratified and simple random sampling to obtain the sample. The sample also comprised 3 deputy principals and 3 teacher counselors who were purposively selected. The research findings showed that the students are involved in academic and co-curricular activities. The study established that perception and discipline are related. It was concluded that there is need to enhance students' involvement in school activities as this has a great influence on students' behavior.