Across the globe, millions of school children struggle with hunger, a significant detriment to their attendance and academic performance. Recognizing this, many countries including Kenya have implemented school meal programs to mitigate hunger, improve attendance and academic outcomes and enhance children’s growth through better nutrition. Despite the program’s success, concerns remain about the safety and quality of food provided to these children. Therefore, this study aimed to assess the awareness of public health officers (PHOs) in Turkana County, Kenya, regarding school meal guidelines, the challenges they face in enforcing food safety regulations and the quality and safety of maize supplied to the program. This study employed a cross-sectional survey of PHOs (n = 35) conducted using a semi-structured questionnaire and sampling of maize from suppliers (n = 22). Mycotoxin analysis and grading of the maize grains were done using recommended methods. The results indicate that only 8.6% of PHOs in Turkana county were aware of the ministry school meal safety guidelines, while 91.4% were unaware of local food safety laws or specific policies that exist for school food. 94.3% of the PHOs pointed out that they struggle to fulfil their duties due to resource limitations such as lack of funding and technical skills as well as logistical obstacles which were vast distances. Also, all the officers indicated that the county lacked a food safety testing facility. Aflatoxin contamination was 24 times higher than the recommended levels in Kenya. These findings clearly show that there is a need to establish food safety monitoring infrastructure as well as capacity building the PHOs in discharging their duties to ensure the health of school children under the program.