Respiratory tract infections (RTIs), caused by microorganisms such as bacteria and viruses, are a leading cause of morbidity and mortality in children worldwide. Antibiotic resistance is a serious concern, and proper prescribing practices are necessary to avoid life-threatening situations. Thus, this study aims to conduct a gender-based analysis and compare antibiotic prescribing patterns for pediatric patients with respiratory tract infections admitted to a tertiary care hospital in Lahore. This comparative cross-sectional study was conducted at Children’s Hospital in Lahore, Pakistan, for three months and enrolled 250 pediatric patients who met the inclusion criteria, including 155 males and 95 females. Data were collected through face-to-face interviews and reviewing hospital records. The results of the study showed that the average number of drugs per prescription was 3.06 ± 1.29 (male) and 3.12 ± 1.5 (female), while the average number of antibiotics per prescription was 2.25 ± 0.60 (male) and 2.17 ± 0.58 (female). The most prevalent medical conditions were bronchopneumonia (53.55% males and 58.95% females), followed by respiratory distress (20.00% males) and pneumonia (16.13% males and 16.84% females). The most commonly prescribed drugs were J01DD04: Ceftriaxone (78.71% males and 71.58% females), J01CR02: Amoxicillin/Clavulanate (59.35% males and 56.84% females), and J01GB06: Amikacin (41.29% males and 45.26% females). A low percentage of prescriptions had major drug-drug interactions (8.39% males and 10.53% females), while most prescriptions had no drug-drug interactions (81.94% males and 84.21% females). There was no significant difference between male and female patients for caregiver, indications for antibiotic prescriptions, the class of active agent prescribed, and drug interactions. Our study findings indicate that most male and female patients admitted to the hospital with lower respiratory tract infections were prescribed antibiotics alongside analgesics and antipyretics. Furthermore, our analysis revealed minimal drug interactions among the prescribed medications. Importantly, we observed a similar antibiotic prescribing trend among male and female pediatric patients, highlighting the consistency in treatment approaches.