The research was carried out in Emgwen division, Nandi central district Kenya with an aim of determining the factors affecting the academic performance of learners with mental deficit in regular schools. All relevant Primary sources were visited in the process of gathering Primary information. A descriptive design was employed and in this case, questionnaires and interview guides were used in the process of data collection. The study findings revealed the following: that the majority of teachers they have no special education training to enable them acquire skills to handle the mentally challenged learners and that it is difficult to obtain resources for the learners with mental retardation. The curriculum they use is not differentiated hence not suitable for the mentally handicapped learners. Recommendations were made which suggested that: Government policies on special needs education be emphasized by the educational officers and provincial administration within the zone that would help to achieve declaration of free primary education for all (FPE) and that schools had to be equipped with the facilities and resources needed to handle learners with mental retardation.