Health service utilization is an important component of child health promotion. Evidence shows that two-thirds of child deaths in low and middle income countries could be prevented if current interventions were adequately utilized. Aim of this study was to identify determinants of variation in health services utilization for children in communities in Nigeria. Multivariable negative binomial regression model attempting to explain observed variability in health services usage in Nigerian communities was applied to the 2013 Nigeria Demographic and Health Survey data. We included the index of maternal deprivation, gender of child, community environmental factor index, and maternal health seeking behaviour, multiple childhood deprivation index and ethnicity diversity index as the independent variables. The outcome variable was under-fives' hospital attendance rates for acute illness. Of the 7577 children from 896 communities in Nigeria that were sick 1936 (25.6%) were taken to the health care facilities for treatment. The final model revealed that both multiple childhood deprivation (incidence rate ratio [IRR] = 1.23, 95% confidence interval [CI] 1.12 to 1.35) and children living in communities with a high ethnic diversity were associated with higher rate of health service use. Maternal health seeking behaviour was associated with a significantly lower rate of health care service use. There are significant variations in health services utilization for sick children across Nigeria communities which appear to be more strongly determined by childhood deprivation factors and maternal health seeking behaviour than by health system functions.