BackgroundMorbidities and mortalities due to malaria can be prevented by the use of insecticide-treated mosquito bed nets (ITN), which has been proven for malaria control and elimination. The purpose of this study was to assess the critical factors that predict the use of ITN among children under-fives in Ghana.MethodsThe study utilized data from the 2019 Ghana Malaria Indicator Survey (GMIS). The outcome variable was mosquito bed net use among children under-fives. To determine critical factors that independently predict ITN use, multilevel multivariable logistic regression was employed using Stata version 16. Odds ratios and associated 95% confidence intervals and p-values were reported. Ap< 0.05 was used to declare statistical significance.ResultsThe overall prevalence of ITN usage was 57.4%. Utilization of bed nets was 66.6% in the rural areas and 43.5% in the urban areas, was highest in the Upper West region (80.6%) even when stratified to rural (82.9%) and urban areas (70.3%) whilst Greater Accra region (30.5%, rural = 41.7%, urban = 28.9%) had the least. The community level multilevel analysis showed that bed net utilization was higher among children in rural areas [AOR = 1.99, 95% CI 1.32–3.01, p = 0.001] and in household with wooden wall materials [AOR = 3.29, 95% CI 1.15–9.40, p = 0.027]. Bed net utilization was however, less for households with 3 + children under-five [AOR = 0.29, 95% CI 0.19–0.46, p < 0.001), 4 years old (AOR = 0.66, 95% CI 00.48–00.92, p = 0.014], without universal access to bed net [AOR = 0.52, 95% CI 0.37–0.73, p < 0.001], those in the Greater Accra [AOR = 0.26, 95% CI 0.13–0.51, p < 0.001], Eastern [AOR = 0.47, 95% CI 0.23–0.95, p = 0.036], Northern [AOR = 0.42, 95% CI 0.20–0.88, p = 0.022], middle [AOR = 0.57, 95% CI 0.35–0.94, p = 0.026] and rich/richest [AOR = 0.51, 95% CI 0.29–0.92, p = 0.025] household wealth quintile. Substantial unobserved household and community level differences in bed net use were found.ConclusionThis study demonstrates the need to intensify promotion of ITN use to those in urban areas, Greater Accra, Eastern and Northern regions, houses without wooden wall materials, middle and rich/richest households. Interventions should be targeted at older children and households with more under-five children and to ensure full access and use of ITNs among all children under-fives in each household as part of the overall goal of achieving the health-related SDGs.