There are concerns with excessive antibiotic prescribing among patients admitted to hospital with COVID-19, increasing antimicrobial resistance (AMR). Most studies have been conducted in adults with limited data on neonates and children, including in Pakistan. A retrospective study was conducted among four referral/tertiary care hospitals, including the clinical manifestations, laboratory findings, the prevalence of bacterial co-infections or secondary bacterial infections and antibiotics prescribed among neonates and children hospitalized due to COVID-19. Among 1237 neonates and children, 511 were admitted to the COVID-19 wards and 433 were finally included in the study. The majority of admitted children were COVID-19-positive (85.9%) with severe COVID-19 (38.2%), and 37.4% were admitted to the ICU. The prevalence of bacterial co-infections or secondary bacterial infections was 3.7%; however, 85.5% were prescribed antibiotics during their hospital stay (average 1.70 ± 0.98 antibiotics per patient). Further, 54.3% were prescribed two antibiotics via the parenteral route (75.5%) for ≤5 days (57.5), with most being ‘Watch’ antibiotics (80.4%). Increased antibiotic prescribing was reported among patients requiring mechanical ventilation and high WBCs, CRP, D-dimer and ferritin levels (p < 0.001). Increased COVID-19 severity, length of stay and hospital setting were significantly associated with antibiotic prescribing (p < 0.001). Excessive antibiotic prescribing among hospitalized neonates and children, despite very low bacterial co-infections or secondary bacterial infections, requires urgent attention to reduce AMR.