Background: The present cross-sectional study was conducted to measure the population attributable risk (PAR) of severe anemia among children aged 6-23 months in the rural district of Kongoussi, in Burkina Faso. Methods: Socio-demographic, clinical, anthropometric, and biological data were collected from children and mothers. Results: In total, 671 children were included in the analysis, 50.4% of whom were male and 97.8% were breastfed. Only 5.8% of the children had adequate complementary feeding, 25.8% were wasted, and 23.5% stunted. Malaria affected about half (50.8%) of children; 39.3% had mild malaria and 11.5% had severe malaria. Children who were no longer breastfed were more likely to have malaria [OR = 3.98 (1.11-14.2), P = 0.022] than those who were breastfed. Fever in the last fortnight [OR = 1.49 (1.07-2.08), P = 0.019], current fever [OR = 4.30 (2.39-7.76), P < 0.001], and presence of splenomegaly [OR = 2.68 (1.54-4.67), P < 0.001] were also positively associated with malaria. Anemia and severe anemia had a prevalence of 96.8% and 24.4%, respectively, and were associated with both mild and severe malaria. Body mass index of mothers [OR = 1.82 (1.06-3.12), P = 0.029], diarrhea in the last fortnight [OR = 1.70 (1.06-2.71), P = 0.027], stunting [OR = 1.54 (1.01-2.34), P = 0.045], and splenomegaly [OR = 2.93 (1.70-5.06), P = 0.045] were other independent factors associated with severe anemia. The PARs of severe anemia due to mild and severe malaria were 22.1% (6.1%-35.4%) and 22.0% (11.6%-27.7%), respectively. Conclusion: Given the high frequency of anemia and severe anemia in this rural malaria-endemic area, interventions are required that consider the important contribution of malaria to anemia and aim to prevent infection.