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Children are more vulnerable to adverse events related to use of drugs. It is therefore important to study drug use in children in order to optimize pharmacotherapy. The aim of this study was to compare drug utilization in paediatric outpatient departments of primary and secondary health care facilities. The patient and drug information of 600 patients was analyzed for World Health Organization (WHO) recommended prescribing indicators. The average number of drugs per prescription was significantly (p < 0.0005) lower in secondary (2.97) compared to primary (3.62) facilities, while average consultation time was shorter (p < 0.0005) in primary than secondary facilities. Percentages of drugs prescribed from Nigerian Essential Drug List (EDL, primary {89.78%}; secondary {91.79%}) and by generic name (primary {55.04%}; secondary {57.88%}) were insignificantly different between the facilities. The use of injectables was low (8.32% in primary versus 3.74% in secondary facilities) while antibiotic use was high (54.14% in primary to 60.28% in secondary facilities). Analysis of the dispensing indicators showed that the secondary facilities were significantly (p < 0.05) better than the primary facilities, even though not a single drug was adequately labeled in both the primary and secondary facilities. Prescription from EDL was found to be fair in the study area while use of injections was low. There is a need for improvement in case of medicines prescribed by generic name.