Background and AimsDespite the implementation of anemia control interventions in Ghana, anemia prevalence is still high in children under‐fives. Reducing the prevalence of anemia requires identifying and targeting associated critical risk factors. This study seeks to identify predictors of anemia among children under‐fives in Ghana.MethodsNationally representative data from the 2019 Ghana Malaria Indicator Survey was used in this study. Both fixed and random effects (multilevel) logistic regression models were applied to 2434 children to identify critical factors associated with anemia.ResultsIn this study, 54% (95% confidence interval [CI] 52.0–57.0) of children under‐5 years were anemic. Infants were more likely to be anemic (66.7%) compared with other children below 5 years. In the multivariable multilevel model, the risk of anemia was found to be higher in younger children especially 6–11 months old (adjusted odds ratio [aOR] = 3.59, CI: 2.54–5.08) and 12–23 months old (aOR = 2.97, CI: 2.08–4.23), children who had malaria (aOR = 1.53, CI: 1.13–2.06), children whose mothers were not registered but not covered with health insurance (aOR = 1.45, CI: 1.21–1.74) or were not even registered for insurance (aOR = 1.49, CI: 1.15–1.93), children born to adolescent mothers (aOR = 2.21, CI: 1.36–3.57), children born to non‐Christian mothers (Islam [aOR = 1.53, CI: 1.17–2.00]), children born to families of poorer households (poorest [aOR = 3.01, CI: 1.64–5.51]; poorer [aOR = 2.56, CI: 1.65–3.98]); middle (aOR = 2.03, CI: 1.32–3.11) and richer (aOR = 1.78, CI: 1.19–2.64), and children who lived in either Upper East (aOR = 2.03, CI: 1.26–3.26) or Central (aOR = 2.52, CI: 1.42–4.47) regions. Significant unobserved community‐level differences in anemia prevalence were observed.ConclusionThe probability of anemia in children under‐fives differs substantially from one community to another, and the prevalence remains high. The identified critical risk factors should be addressed. Multifaceted and targeted approaches are needed to help reduce the anemia prevalence in this setting to achieve the multiple United Nation's Sustainable Development Goals, which are related to risk and prevalence of anemia by 2030.