Proton pump inhibitors (PPIs) are used as prophylaxis, guarding against anastomotic stricture (AS) in the aftermath of reconstructed esophageal atresia (EA). The incidence of stricture formation was studied in this setting, comparing outcomes of 3- and 12-month PPI prophylactic regimens. Patient characteristics (gestational age, birth weight, prevalence of chromosomal aberrations, and other malformations), as well as rates of survival, AS formation, and required balloon dilation, were recorded in the following therapeutic subsets: (1) all infants undergoing primary surgical anastomosis for EA in years 2010-2014 and given postoperative PPI prophylaxis for 12 months and (2) all infants similarly treated for EA in years 2001-2009 but given postoperative PPI prophylaxis for 3 months only. Duration of follow-up was 1 year in each group. Patient characteristics and survival rates in 12-month ( = 33) and in 3-month ( = 30) treatment groups did not differ significantly. The prevalence of AS was 42%/43% in each group (12 months, 14/33; 3 months, 13/30; = 1). Median number of dilations required was 3 (range, 1-9) per patient in each group ( = 0.69). Median age at initial dilation was 163 days and 63 days in 12- and 3-month groups, respectively ( = 0.04). Development of AS in the first year after reconstruction of EA was not reduced by prolonged PPI prophylaxis (12 vs. 3 months), but initial balloon dilation procedures were performed later in infants who were treated longer.