Abstract The inability of perfect system to promote student discipline in Kenyan secondary schools necessitated the introduction of Student Council system by the Ministry of Education in 2008, to make student leadership more participatory. Although Student Councils were introduced to enhance student participation in school governance and to avert previous cases of student unrest, concerns have been raised over the effectiveness of the Student Council system. This study sought to establish the issues and challenges confronting Student Councils, particularly, focusing on Bungoma North Sub-County. The target population of the study was 40 public secondary schools, 40 Deputy Principals, 400 teachers, 12000 students, and 1,324 members of Student Councils. The sample selected included 10 Deputy Principals, 100 teachers, 102 members of the Student Council, and 600 students. The study design included stratified sampling to obtain 10 schools that were used for the study. Interview schedules, survey questionnaires and focus group discussion guides were study instruments used in the collection of data. Pilot-testing with the instruments was conducted at two schools. The researcher found 258 MAXIMIZING EDUCATIONAL CHANGE out that Student Councils were facing challenges, such as inadequate support in their roles, opposition from students and teachers, lack of team-work among Student Council members, low motivation and isolation by other students. The school administrators will use these findings as a basis for assessing the status of Student Councils in their respective schools and address the challenges facing Student Councils using the suggested strategies. The study recommends that Student Council members should be exposed to more induction and leadership courses to improve upon their leadership skills. Keywords: Students Councils, challenges, effectiveness