Background: Pyloric botulinum toxin injection has improved symptoms in children with delayed gastric emptying. We aimed to determine the clinical response to combined endoscopic intra-pyloric botulinum toxin injection and pyloric balloon dilation (IPBT-BD) in patients with dyspepsia. Methods: Electronic medical records were reviewed to gather demographic data, symptoms, and follow-up on patients with dyspepsia. Cases were defined as those who underwent IPBT-BD in addition to their ongoing management. Controls received pharmacotherapy, behavioral intervention, or dietary management alone. Clinical response was defined as no change, partial, or complete improvement in symptoms within 12 months. Propensity score matching based on age, gender, and symptom duration was used to pair cases and controls. Results: In total, 79 cases and 83 controls were identified. After propensity matching, 63 patients were included in each group. The mean age for cases was 14.5 ± 3.9y; 62% were females and 98% were Caucasian. Further, 83% of 46 cases and 94% of 49 controls who had scintigraphy scans showed delayed gastric emptying. After matching, 76% of cases showed partial or complete improvement compared with 49% controls within 12 months ( P = 0.004). Younger children tended to respond more favorably to the procedure ( P = 0.08). Conclusions: In our propensity-matched analysis, combined IPBT-BD in addition to pharmacotherapy, behavioral, or dietary management clearly showed a benefit over these modalities alone. This favorable response lasted up to 12 months.