BACKGROUND: An esophageal anastomotic stricture (EAS) after an esophageal atresia surgery occurs in approximately 4-60% of the cases, and its first-line therapy includes balloon dilatation. Oral balloon dilatation cannot be performed in some EAS cases; conversely, even if dilatation is possible, these strictures recur in some cases, necessitating a surgical procedure for repairing the stenosis. However, these procedures are invasive and have short- and long-term complications. If an EAS recurs repeatedly after multiple balloon dilations, gastroesophageal reflux disease (GERD) may be the underlying cause. A fundoplication procedure may be effective for treating a refractory EAS, as in the present case. CASE PRESENTATION: A neonatal patient with type D esophageal atresia underwent thoracoscopic esophago-esophageal anastomosis at the age of 1 day, and her postoperative course was uneventful. Thereafter, the patient underwent gastrostomy for poor oral intake at the age of 3 months. After gastrostomy, the patient presented with a complete obstructive EAS. Balloon dilatation via the oral route was attempted; however, a guidewire could not be inserted into the EAS site. Hence, retrograde balloon dilatation via gastrostomy was performed successfully. However, the EAS recurred easily thereafter, and laparoscopic anti-reflux surgery was performed to prevent GERD. The anti-reflux surgery cured the otherwise refractory EAS and prevented its recurrence. CONCLUSIONS: Retrograde balloon dilatation is another treatment option for an EAS. When an EAS recurs soon after dilatation, the patient must be evaluated for GERD; if severe GERD is observed, an appropriate anti-reflux surgery is required before dilating the EAS.