Peace and tranquility is paramount for the success of any entity. Unrest in Kenyan secondary schools has contributed to great damage through wanton destruction and has led to low performance, a factor that has had many parents, teachers, educationists, scholars and the Kenya government concerned. The general objective of this study was to analyze the factors contributing to students’ unrest in Kenyan secondary schools with a specific focus on selected Counties with a view of recommending possible solutions in dealing with this emerging phenomenon. The study was guided by the following specific objectives; establish the extent to which students’ socio-cultural background contributes to unrest in secondary schools in Kenya, determine the extent to which psychoactive substance use contributes to students’ unrest in secondary schools in Kenya, assess the relationship between communication and students’ unrest in secondary schools in Kenya, establish the extent to which abdication of parental responsibilities influence unrest in secondary school in Kenya, and determine the extent to which rules and regulations influence students’ unrest in secondary school in Kenya. A descriptive and cross-sectional survey design was used for this study. A random sample of 1,380 participants was sampled from Schools that experienced student unrest in Kisii, Nyamira, Kericho, Uasin Gishu, Embu, and Nakuru Counties between March and August 2016. Government policy required that permission be granted by the Principal Secretary in the Ministry of Education before collecting data. The letter issued by the Principal Secretary was availed to all County and Sub County Education Coordinators, and the schools Principals for the smooth follow of the process. Research assistants were used to help in the administration of the semi structured questionnaires due to the expansive nature of participating counties. The questionnaire enabled the researcher collect both quantitative and qualitative data. More qualitative data was collected from school Principals by use of an interview guide. Multivariate statistical methods were used to analyze quantitative data while content analysis was used to analyze qualitative data. Findings report a significant positive relationship between the study independent variables socio-cultural background, psychoactive substance abuse, communication, parental abdication of responsibilities, rules and regulations, and the dependent variable school unrest and its disruptive consequences in Kenya’s secondary schools. The study provides several recommendations that may guide policy and practice for key stakeholders that could help deal with student unrest in Kenya’s secondary schools.