There has been a growing concern in Kenya that boys have gradually been left out of the gender equation with little research capturing their schooling experiences. When examined, boys' underachievement is treated with suspicion that has led to few studies demonstrating their marginalisation. This paper explored the manifestations of boys' underachievement in education in Busia and Kirinyaga counties in Kenya. The study was carried out in 12 primary schools targeted 12 headteachers, 24 teachers, 480 pupils, 8 education officials and 180 households. Enrolment, school attendance, and candidature for national examinations data showed boys were marginalised. In addition, they lacked adequate role models. However, on performance, boys still had better results than girls. The paper concludes that boys were beginning to under participate in education and recommends the need for gender interventions to target both boys and girls and tripartite efforts at communities, county governments and national government to re-enrol boys.