There have been current controversial discussions concerning the performance of private primary schools versus public primary schools in the Kenya Certificate of Primary Examination (K.C.P.E.). Lately, the private primary schools appear to be performing better than public primary schools. For example; in the 2003 K.C.P.E. results, more than 31% of the top 100 candidates came from private schools; in the 2004 K.C.P.E. results, more than 92% of the top 100 candidates came from private schools. In January 2005, 68% of admissions to national schools came from private schools (MOEST, 2005). In 2006, though more than 60% of the top 100 positions were taken by private schools most of the public primary schools showed improvement. This performance has elicited all kinds of reactions from political leaders and educationists. Among them the question; why are the performances as such? And what factors contribute to the performances? This paper therefore sought to establish the factors that contribute to the current academic performance of these schools. The paper made use of ex post facto research design. Simple random sampling was used to select eight public and eight private primary schools in Kitale Municipality. Through interviews and questionnaires the teachers and the administrators provided information on enrollment, academic performance, teacher-pupil ratio and factors leading to the current performance. The work was based on the systems theory which postulates that a school is like a factory that has inputs and outputs. Inputs have to undergo a process and outputs tested for their quality. It justifies the use of tests as a measure of academic performance. The government needs to step up financial and material support to public schools to cater for high enrollment due to F.P.E. program. It is hoped that educational stakeholders including teachers, parents, policy makers and students will benefit from the study.