This study investigated anemia prevalence and associated factors using a cross-sectional approach with 429 children 6 to 59 months of age in Jordão, Acre State, Brazil. Multiple Poisson regression in hierarchical models was used in the analysis. Overall anemia prevalence was 57.3% (95%CI: 52.5%-2.1%). Age under 24 months [prevalence ratio - PR (95%CI): 1.40 (1.09-1.74)], living in rural areas [PR: 1.23 (1.04-1.44)], households with 5-14 children [PR: 1.23 (1.04-1.44)], stunting [PR: 1.19 (1.01-1.39)], maternal anemia [PR: 1.18 (1.00-1.39)], and smoking during pregnancy [PR: 1.29 (1.09-1.53)] were associated with increased risk of anemia. Children of working mothers were at lower risk of anemia [PR: 0.78 (0.64-0.94)]. Anemia prevalence in childhood was found to be a serious public health problem in this municipality. Multi-sector prevention strategies should be implemented, addressing poverty and maternal-infant healthcare.