Introduction: Jejunoileal atresia (JIA) is a common cause of neonatal intestinal obstruction and is a common surgical emergency. The aim of this study was to compare primary anastomosis without resection of the dilated segment with transanastomotic T tube jejunostomy (TATTO) versus resection of the dilated segment without T tube as the control group for treatment of patients with JIA. Material and Methods: During 2008 to 2013, 105 patients were diagnosed with JIA at the time of surgery and were recruited for this study. Data relating to efficacy and procedural complications were compared among patients. The criteria for exclusion were duodenal obstruction, colonic atresia, intestinal perforation, malrotation, and also JIA patients with associated other anomalies like meconium ileous, gastroschisis and anorectal malformation. Results: A total of 125 patients were diagnosed and 16 patients were excluded. Our patients were divided into a control group (n=52) and a TATTO group (n=57). The TATTO group had a significantly shorter postoperative hospital stay (12 vs. 23 days, p=0.001) and time to start feeding (9 vs. 13 days, p=0.003) compared with the control group. Sepsis (12.0% vs. 32.7% p=0.004), other complications (3.6% vs. 15.4% p=0.001) and the associated morbidity were significantly lower in the TATTO group. Conclusion: The findings suggest that the TATTO technique was a better method for the treatment of children with JIA, as study showed lesser morbidity and mortality rates.