Background Pneumonia causes about 0.9 million deaths worldwide each year. The World Health Organization (WHO) guidelines for the standard management of severe pneumonia requires parenteral ampicillin every 6 hours and once-daily parenteral gentamicin for 5 to 7 days. Although this treatment has contributed to the reduction of mortality, it requires nursing interventions every 6 hours for 7 days. Further intervention trials should be conducted to search for alternate antibiotics with better adherence, reduced cost, and reduced hospital stay. Parenteral amoxicillin is an effective alternative to ampicillin, as it has a longer half-life and broader coverage. Objective The aim of this clinical trial is to compare the efficacy of a dose of injectable amoxicillin every 12 hours plus a once-daily dose of injectable gentamicin with a dose of injectable ampicillin every 6 hours plus a once-daily dose of injectable gentamicin in children hospitalized for severe pneumonia. Methods This randomized, controlled, open-label, noninferiority trial is being conducted in Dhaka Hospital of the International Centre for Diarrheal Disease Research, Bangladesh. A sample size of 308 children with severe pneumonia will give adequate power to this study. Children aged 2 to 59 months are randomized to either intravenous ampicillin or intravenous amoxicillin, plus intravenous gentamicin in both study arms. The monitoring of the patients is carried out according to the WHO protocol for the treatment of severe pneumonia. The primary objective is the rate of treatment failure, defined by the persistence of danger signs of severe pneumonia beyond 48 hours or deterioration within 24 hours of initiation of the therapy. The secondary objectives are (1) improvement in or the resolution of danger signs since enrollment, (2) length of hospital stay, (3) death during hospitalization, and (4) rate of nosocomial infections. Results Enrollment in the study started on January 1, 2018, and ended on October 31, 2019. Data entry and analysis are in progress. Findings from the study are expected to be disseminated in October 2020. Conclusions Our study's findings will improve compliance with the use of antibiotics that require less frequent doses for the treatment of severe pneumonia. Trial Registration ClinicalTrials.gov NCT03369093; https://clinicaltrials.gov/ct2/show/NCT03369093 International Registered Report Identifier (IRRID) DERR1-10.2196/17735