BackgroundEvery 75 seconds, a child under five dies of malaria. Mainly children, aged between six months and five years, are at the highest risk for malaria. These children lost maternal immunity and did not yet developed specific immunity to the infection. Under the age of five, children bear the highest burden of malaria in Sub-Saharan Africa (SSA). Many individual and community level factors could contribute to malaria prevalence remaining high among under-five children in the region. Thus, this study aimed to assess the pooled prevalence of malaria among children aged 6–59 months and identify potential factors associated with malaria by using recent Malaria Indicator Surveys in 13 SSA countries.MethodsData for this study were drawn from recent 13 Sub-Saharan African countries Malaria Indicator Surveys (MIS). A total weighted sample of 60,541 children aged 6–59 months was included. STATA version 14.2 was used to clean, code and analyze the data. Multilevel logistic regression was employed to identify factors associated with malaria. Adjusted odds ratio with 95% CI and a P value <0.05 was reported to indicate statistical association. Model fitness and comparison were done using Inter cluster correlation coefficient, Median odds ratio, proportional change in variance, and deviance.ResultsThe pooled prevalence of malaria among children aged 6–59 months was found to be 27.41% (95% CI: 17.94%-36.88%). It ranges from 5.04% in Senegal to 62.57% in Sierra Leone. Aged 36–47 months (AOR = 3.54, 95% CI 3.21–3.91), and 48–59 months (AOR = 4.32, 95% CI 3.91–4.77), mothers attended primary education (AOR = 0.78, 95% CI 0.73–0.84), richer (AOR = 0.35, 95% CI 0.32–0.39), and richest household (AOR = 0.16, 95% CI 0.14–0.19), number of three and more under-five children (AOR = 1.35, 95% CI 1.26–1.45), improved floor material (AOR = 0.65, 95% CI 0.57–0.73), improved wall material (AOR = 0.73, 95% CI 0.64–0.84), improved roof material (AOR = 0.70, 95% CI 0.51–0.93), insecticide-treated bed net (ITN) use (0.56, 95% CI 0.51–0.62), not anemic (AOR = 0.05, 95% CI 0.04–0.06), rural resident (AOR = 2.16, 95% CI 2.06–2.27), high community ITN use (AOR = 0.40, 95% CI 0.24–0.63) and high community poverty (AOR = 2.66, 95% CI 2.53–2.84) were strongly associated with malaria.Conclusions and recommendationsAlmost 3 out of 10 children were infected by malaria in 13 SSA countries. Malaria infection remains one of the main killers of children aged 6–59 months in the SSA. This study revealed that older under-five children living in large families with low incomes in rural areas are most vulnerable to malaria infection. Our results clearly indicate that ITN utilization and improved housing are promising means to effectively prevent malaria infection among children aged 6–59 months. It is therefore important to note that households with low wealth quintiles and rural residents should be prioritized in any mass distribution of ITNs. This has to be accompanied by education using mass media to enhance community awareness.