Kenyan government launched Free Primary Education (FPE) in 2003 to make schooling affordable to all parents, but less attention has been paid to the quality assurance and equity of the education system. Studies have indicated that the FPE policy sacrificed the quality of education and this led to parents avoiding FPE offered in primary schools and take their children to private schools which are very costly. This study adopted descriptive survey design to as the research design. Rational comprehensive model theory was used which aims at discussing factors influencing parental choice between private and public primary schools in Rachuonyo Sub-County. The study endeavored to achieve the following objectives first, to investigate the influence of academic factors on parental choice second, to determine how personal factors influence parental preference third, to examine the influence of policy factors on parental preference and lastly to explore the influence of ideological factors on parental preference. The accessible population for this study was 5269 parents and 198 head teachers out of which 240 respondents 200 were randomly selected from parents and 40 respondents were from head teachers. The sample size from the sampled schools was done using stratified random sampling. Questionnaires and interview schedules were used as the main data collection tools. Validity and reliability was ascertained by the internal consistency and piloting. Trustworthiness and authenticity of qualitative data was enhanced by adopting credibility, transferability, dependability and conformability of the data. The quantitative data was analyzed using data analysis matrix while the qualitative data was analyzed through t-hematic analysis. The study found out that, in academic factors, parents looked at prestige in school performance; chances of pupil performance improvement; and curriculum organization and management. On personal factors, parents consider mainly healthy environment, teacher-pupil relationship and travel distance to school. On policy factors, parents considered efficient use of facilities and space; administrative leadership philosophy; security and innovativeness; government funding, fees and scholarship; and enrolment policy. Ideologically, parents considered interactions with the community; clan factor in school activities; the school religious sponsor; enhanced parents participation; and the political alignment of the management.