The challenge of countering violent extremism in Africa attributes to the non-inclusion of the various actors and the different spaces that provide vulnerabilities to radicalization and recruitment into terrorism. There is a lot on the topic of radicalization and recruitment happening among school going children based on the increasing disappearances, indiscipline cases and arrests of school going children linked to extremist organizations. However, most of these incidences backed with valuable research and documented data. This research examines and analyzes the key challenges for countering terrorism and in particular the role of the school environment as a space for the youth radicalization and recruitment to terrorism. The research uses conversion theory to examine the processes that underpin radicalization and recruitment into Terrorism by reviewing fieldwork data from eight selected secondary school in Nairobi and Kakamega. The assumption of its application tests the rationality, emotional levels as social factors coupled with other economic and/or political factors in the children are areas of consideration in the radicalization process that leads to terrorism. Using mixed methodology the research found out that radicalization and recruitment processes are taking place in secondary schools; students mention two students as suspects who have joined Al-Shabaab, gangs like the Gaza group, are operational in schools and an average 42% of the students think that the administrations are not aware of what is happening. The research has three categories of recommendations including; oversight authority to is strengthened at the school level, background checks to service providers, review of student transfers and minimized leadership responsibilities to new students until the probation period of one term is done and encourage more responsibilities for the parents. The study also recommends that the government through the ministry of education and the National Counter Terrorism Center provide capacity building on early warning signs, provide a mechanism for reporting and Gazette school to religious institution affiliations for the authorization of preachers and other religious service providers. Finally, the research recommends more research on the relationship between poverty and terrorism, government responses to learning institutions about countering terrorism and the relationship between gangs and terrorism in schools.