Drug utilization in Neonatal Intensive Care Units is complex due to the immaturity of neonates and the critical nature of their ailments. Understanding prescribing patterns is essential for promoting rational pharmacotherapy and improving neonatal outcomes. To evaluate drug utilization patterns in the Neonatal Intensive Care Unit at Aljala Maternity and Gynecology Hospital, Tripoli, Libya. A prospective, cross-sectional observational study was conducted from September to December 2023. Data were collected from 503 neonates who received at least one medication. Drug use was analyzed based on the World Health Organization-Anatomical Therapeutic Chemical classification. Of 739 neonates admitted, 503 met the inclusion criteria. Males accounted for 57.3% and 73.0% were born at term. The average hospital stay was 5.61 days. Neonatal sepsis (87.5%) and respiratory distress (65.2%) were the most common diagnoses. A total of 1,443 medications were prescribed, with an average of 2.9 drugs per neonate. Anti-infective agents represented 79.8% of all prescriptions, with benzyl penicillin, gentamicin, and cefotaxime being the most common. Injections were used in 93.1% of cases, and 97.4% of drugs were from the Libyan Essential Medicines List. The findings reveal high antibiotic use and empirical prescribing practices in response to infectious morbidities. There is a critical need for improved diagnostic support, therapeutic drug monitoring, and antimicrobial stewardship to ensure safe and effective pharmacotherapy in the Neonatal Intensive Care Unit.