Although considerable global initiatives have been undertaken to tackle anaemia, its prevalence continues to be high in sub-Saharan African nations. In Mali specifically, anaemia represents a significant and pressing public health issue. The purpose of the present study was to examine the key risk factors related to anaemia among children aged 6–24 months (younger age group) and 25–59 months (older age group). We used the Mali 2018 Demographic and Health Survey data, collected from 8861 mothers with children under five. Logistic regression was used to assess the risk factors for childhood anaemia. The results suggest that the prevalence of anaemia was 88 % in the younger and 76 % in the older age groups. The risk factors unique to the younger age group were malaria (OR 4⋅05; CI 0⋅95, 11⋅3) and place of residence (OR 0⋅55; CI 0⋅32, 0⋅94), while for the older age group, they were morbidity (OR 1⋅91; CI 1⋅12, 3⋅24), drinking from a bottle (OR 1⋅52; CI 1⋅04, 2⋅22), and micronutrient intake (OR 0⋅61; CI 0⋅40, 0⋅91). Risk factors that significantly contributed to both age groups include breastfeeding, deworming, maternal anaemia, maternal education, and wealth index. Anaemia also varied by region. The widespread prevalence of anaemia can be attributed to a multitude of factors. In addressing this issue, it is imperative to acknowledge the unique characteristics of specific regions and rural areas, where the incidence of anaemia surpasses the national average. Therefore, any intervention efforts should be tailored to the specific needs and challenges of these areas.