Background/objectives: Antimicrobial stewardship (AMS) is essential to optimize antibiotic use and limit antimicrobial resistance (AMR), particularly in pediatric populations where diagnostic uncertainty and system constraints complicate care. This study investigated critical AMS indicators, namely, missed antibiotic doses, microbiological diagnostics, and antibiotic prescribing at hospital discharge, which are key challenges that may affect treatment outcomes in hospitalized children under five years old. Methods: A prospective descriptive study was conducted in two tertiary pediatric hospitals in Zambia among children aged 29 days to 59 months. Information on missed antibiotic doses, microbiological investigations, and antibiotic prescribing at discharge from hospitalization was obtained from medical records and medication charts. Results: Patients experienced 1–8 missed doses, most commonly involving benzylpenicillin and ceftriaxone. Documentation of reasons for missed doses was largely absent. Microbiological testing was requested in 36.6% of patients, but only 14.8% of antibiotic prescriptions were supported by culture and susceptibility testing. Of requested tests, 80.9% of results were unavailable at discharge, limiting clinical utility. Only 19.1% of results were available, with a low culture positivity rate (27.3%). Overall, 41.8% of patients were discharged on antibiotics, predominantly from the WHO “Access” group (78%), though 22% were “Watch” antibiotics, and none from the “Reserve” group. Shorter hospital stay was significantly associated with discharge antibiotic prescribing (p = 0.0079; χ2 = 78.577, p < 0.001). Conclusions: Significant AMS gaps exist, including frequent missed doses, limited diagnostic support, and high discharge antibiotic use. Strengthening medication administration systems, improving laboratory capacity and turnaround times, and optimizing discharge prescribing are critical for enhancing pediatric AMS and reducing AMR.