Background Diarrhea is the second-leading cause of death in children under 5 years of age. In low- and middle-income countries, 3%-20% of acute diarrheal episodes become persistent diarrhea (PD) (ie, duration ≥14 days), which results in 36%-56% of all diarrheal deaths. In Bangladesh, PD causes >25% of diarrhea-related deaths. Commensal gut microbiota dysbiosis is increasingly recognized in the pathogenesis of PD. Hospital-based management of PD requires a hospital stay, which increases the risk of infection and hospital costs. The higher cost of treatment and high case-fatality rates reiterate PD as an important public health problem. At the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), for the last two decades, a consensus-based guideline has been followed for PD. Observation has revealed that green banana helps in the resolution of diarrhea. However, no larger prospective study has been conducted to evaluate the efficacy of green banana in the management of PD among children older than 6 months of age. Objective Our objective is to assess the efficacy of full-strength rice suji with and without green banana compared to three-quarter-strength rice suji in the management of PD in children aged 6-36 months at the Dhaka Hospital of the icddr,b. Methods This open-labeled, randomized controlled study aims to enroll a total of 145 children with PD who have not been improving on a diet of milk suji. Children will be randomized into three different diet-specific groups: full-strength rice suji containing green banana, full-strength rice suji alone, and three-quarter-strength rice suji. The primary outcome is the percentage of children who recovered from diarrhea by day 5. Results Recruitment and data collection began in December 2017 and were completed in November 2019. Results are expected by April 2020. Conclusions This study is expected to provide insights into the incorporation of green banana into the dietary management of PD. This would be the first study to investigate the role of microbiota and metabolomics in the pathogenesis of PD. Trial Registration ClinicalTrials.gov NCT03366740; https://clinicaltrials.gov/ct2/show/NCT03366740 International Registered Report Identifier (IRRID) DERR1-10.2196/15759