Using high resolution impedance manometry (HRIM), this study characterized the esophago-gastric junction (EGJ) dynamics in children with esophageal atresia (EA). Esophageal HRIM was performed in patients with EA aged less than 18 years. Objective motility patterns were analyzed, and EGJ data reported. Controls were pediatric patients without EA undergoing investigations for consideration of fundoplication surgery. Seventy-five patients (M:F = 43:32, median age 1 year 3 months [3 months-17 years 4 months]) completed 133 HRIM studies. The majority (64/75, 85.3%) had EA with distal tracheo-esophageal fistula. Compared with controls, liquid swallows were poorer in patients with EA, as evident by significant differences in distension pressure emptying and bolus flow time (BFT). The integrated relaxation pressure for thin liquid swallows was significantly different between EA types, as well as when comparing patients with EA with and without previous esophageal dilatations. The BFT for solid swallows was significantly different when compared with EA types. We have utilized HRIM in patients with EA to demonstrate abnormalities in their long-term EGJ function. These abnormalities correlate with poorer esophageal compliance and reduced esophageal peristalsis across the EGJ. Understanding the EGJ function in patients with EA will allow us to tailor long-term management to specific patients.