<p>Fungal contamination of cereal foods is a significant food safety concern in many sub-Saharan African countries, including Namibia, where cereals are a staple in children’s diets and crucial for food security. Cereals are highly susceptible to fungal infestation and mycotoxin accumulation throughout cultivation, storage, and processing, posing serious health concern, particularly to vulnerable children. Although food-borne illnesses are reported in northern Namibia, limited research exists on fungal contamination in cereals consumed by rural households. This study aimed to determine the occurrence of fungal species in processed cereal foods consumed by children under five years in Oshana region in 2021 and 2023. Additionally, awareness of fungal contamination and food handling practices in rural households was documented. A cross-sectional quantitative design was employed, involving 207 purposively selected rural households. Processed cereal food samples (<i>n</i> = 207), including flour and ready-to-eat foods, were analyzed for fungal species. Data on fungal contamination awareness and food handling practices was collected through validated structured questionnaires. Cereal flour samples harbored greater fungal richness (18 species) compared to ready-to-eat foods (6 species). Molecular analysis identified 18 fungal species, predominantly <i>Aspergillus</i> (72%), <i>Fusarium</i> (15%), and <i>Penicillium</i> (6%). Despite that 94% of respondents acknowledged the presence of fungal contamination in food, and 72% consented to practicing proper food handling techniques, the fungal contamination level observed highlights gaps in these practices. The findings emphasize the urgent need to educate rural farmers in Oshana on proper food handling and storage techniques to mitigate fungal and mycotoxin contamination risks and ensure food safety for children.</p>