Aflatoxins are mycotoxins that can contaminate grains, legumes, and oil seeds. These toxic compounds are an especially serious problem in tropical and sub-tropical climates. The objective of this study was to raise awareness of aflatoxin exposure among primary school children in Shebedino woreda, southern Ethiopia, by measuring urinary aflatoxin M1 (AFM1). The study employed a cross-sectional design and systematic random sampling of children from eight schools in the district. The mean ± SD age of the children was 9.0 ± 1.8 years. Most (84.6%) households were food insecure with 17.9% severely food insecure. Urinary AFM1 was detected in more than 93% of the children. The median [IQR] concentration of AFM1/Creat was 480 [203, 1085] pg/mg. Based on a multiple regression analysis: DDS, consumption of haricot bean or milk, source of drinking water, maternal education, and household food insecurity access scale scores were significantly associated with urinary AFM1/Creat. In conclusion, a high prevalence of urinary AFM1 was observed in this study. However, the relation between AFM1 and dietary intake was analyzed based on self-reported dietary data; hence, all of the staple foods as well as animal feeds in the study area should be assessed for aflatoxin contamination.