Background: Vitamin A deficiency (VAD) is still a public health problem across the globe and also in Burkina Faso, especially for under-five-years-old children. Since less information is available about the prevalence of VAD among the primary school children, this study aimed to study this area. Methods: A randomised double-blind placebo-controlled trial was conducted to assess the effect of high dose of vitamin A (VA) and daily zinc versus high dose of VA and daily zinc placebo (6 days per week) during four months among the primary school children. Of the total number of 200 school children, 100 were allocated to two random groups. Participants’ gender, age, weight, and height were measured, a blood smear was performed for malaria diagnosis, stool samples were collected for intestine parasites’ assessment, and blood samples were collected for haemoglobin and serum retinol measurement. Results: Baseline data of 183 school children were analysed and the findings showed that 20.6% of the school children were underweight (23.2% in girls vs. 16.5% in boys; P = 0.043). Anemia affected 36.2%, 39% had Plasmodium Falciparum, and 37.6% had intestine parasites. Furthermore, VAD prevalence was 46.1% (51.0% in boys vs. 41.2% in girls; P = 0,072). Conclusion: Among primary school children in the Western part of Burkina Faso, VAD is not only higher than other regions of the country, but also twice the critical level and defined as a severe public health problem by WHO. This result calls for action among the primary school children and recalls the importance of taking strategies against VAD among under-five-year-old children.