A healthy and conducive learning environment, safe drinking water, and child-friendly sanitation facilities in the school where children spend time are necessary. However, children do not use the toilets regularly due to lack of privacy, poor cleanliness, smell, and lack of toilet paper, soap, and hand-drying materials. The study aimed to establish the factors influencing the implementation of sanitation policy guidelines as stated in the Kenya School Health Policy and the Safety Standards Manual for schools on the sanitation facilities in the public primary schools in Meru County which is in a rural-urban setting. The study aimed to ascertain the student toilet ratio, status of awareness on sanitation issues, environmental sanitation, and regular inspection of the primary schools on the implementation of sanitation guidelines. The study was grounded on the Theory of Planned Behaviour and The Hubley’s BASNEF model theories. To achieve its objectives, the study adopted a descriptive survey design. A sample of 159 schools was selected from a total of 773 primary schools in Meru County using simple random sampling. Data was collected using a Structured Direct Observation Schedule and questionnaire. Data were analyzed using SPSS version 26.0 software. Descriptive statistics including mean and cross-tabulations were used. Pearson’s Chi-Square test was used to determine relationships between the variables. The study revealed that the boy’s toilet ratio was 22:1 while the girls were 17.1 which is within the recommended ratios. 46.7% remained neutral regarding stakeholder awareness which hinders the enforcement of policy.31.4% disagreed the availability of clear parents and children's roles to ensure a clean school environment. 29.5% needed clarification regarding the frequency and effectiveness of inspections. The study concluded that sanitation structures need to be cleaned regularly by a staff employed by the school. The dissemination of sanitation guidelines promotes stakeholders’ engagement and shares sanitation-related information with the children. There is a need for a clear budget for sanitation, sensitize teachers, add sanitation facilities, and enhance the clarity and effectiveness of inspections in primary schools. The study recommended that similar studies be done in other counties.