The introduction of Free Primary Education (FPE) policy in 2003 was aimed at enhancing the enrolment of all school going-age children in Kenya indiscriminately. However, significant concerns have been raised by scholars and the public over the low enrolment of children with Special Needs Education (SNE). The main objective of this study was to determine the efficacy of FPE policy on enrolment of special needs children in education in West Pokot County, Kenya. Descriptive survey research design was used. The target population was 696 respondents drawn from the 65 primary schools, SNE teachers of West Pokot County. Purposively sampling was used due to relatively low enrolment of children with special education needs. Simple random sampling was used to obtain the respondents as follows: 362 pupils with SNE and 123 SNE teachers. Each sub-county formed an important cluster from where the respondents were drawn from. The researcher collected data from pupils with special needs education and special education teachers. Focused Group Discussions (FGD), Document Analysis schedule and interview schedules were also used during the study. Content validity was done through the contributions of experts in the Department of Educational Planning and Management of Masinde Muliro University of Science and Technology. Pilot study was carried out to establish the reliability of the instruments. Test-retest method was employed to obtain the reliability of the instruments at 0.05 level of confidence. The findings yielded both qualitative and quantitative data and presented in frequency tables and line graphs. The findings revealed that factors affecting the efficacy of free primary education range from; sociocultural, economic, environmental, school based, individual and policy and system factors. The study thus recommends that the government commits more resources to FPE financing policy and employ strategic and individualized mechanisms such as early identification, screening, tracking and monitoring of pupils from homesteads to homestead to ensure enrolment enhanced nationally.