The Government of Kenya introduced Free Day Secondary Education Programme in 2008. Although this enabled many primary school leavers to continue their education, public secondary schools are facing with significant challenges in terms of human, financial and physical resources. The purpose of this paper is to explore the extent of challenges that public secondary schools are facing with and how they overcome these challenges in order to improve academic performance. The study employed a case study approach with questionnaires and semi-structured interviews with teachers and visited 11 public schools at Imenti South sub-county in Meru in 2013/14. Findings reveal that despite increasing enrolments, teacher shortfalls and insufficient facilities and teaching and learning materials, some schools in Imenti South sub-county still show an improvement trend in academic performance due to the sub-county’s and schools’ initiatives in various practices and shared responsibilities among all stakeholders.