ABSTRACT Objectives: Proton pump inhibitor (PPI)‐responsive eosinophilic esophagitis (EoE) is frequently observed in children, but data on long‐term treatment are scarce. The objective of this study is to evaluate the long‐term efficacy and safety of PPIs in children with EoE. Methods: This prospective study enrolled children with EoE and histological remission to an 8‐week esomeprazole trial (1 mg/kg/dose, twice daily). Esomeprazole was maintained at 1 mg/kg/day for 1 year. Symptom recurrence and adverse events were monitored and a follow‐up endoscopy was performed at 12 months. Complete histological remission was defined as ⩽5 eosinophils/high‐power field (eos/hpf), and partial histological remission as >5 and <15 eos/hpf. Patients had no concomitant dietary restrictions or topical steroid. Results: Fifty‐seven children were included. Histological remission on maintenance PPI therapy was present in 40 children (70.1%; 95% CI 56.5–81.5). Long‐term remission rate was higher in children with initial complete histological remission than in those with partial remission (81% vs 50%, P = 0.014). Forty‐nine children (86%) remained asymptomatic. Pretreatment clinical and histological findings and median PPI dose/kg/day were similar between relapsers and nonrelapsers. Eleven out of 12 children (91.6%) receiving esomeprazole 0.5 mg · kg −1 · day −1 for 12 additional months remained in remission. Mild and transient side effects without requiring PPI avoidance were observed in 5 children. Conclusions: Up to 70% of children with PPI‐responsive EoE remain in histological and clinical remission on a low‐dose maintenance treatment at 1‐year follow‐up, with adequate safety profile. Complete histological remission to an 8‐week PPI trial was associated with higher probability of histological remission on maintenance therapy.