Junctional ectopic tachycardia (JET) is an arrhythmia observed almost exclusively after open heart surgery in children. Current literature on JET has not focused on patients at the highest risk of both developing and being negatively impacted by JET. The purpose of this study was to determine the overall incidence of JET in an infant patient cohort undergoing open cardiac surgery, to identify patient- and procedure-related factors associated with developing JET, and to assess the clinical impact of JET on patient outcomes. We performed a nested case-control study from the complete cohort of patients at our institution younger than 1 year of age who underwent open heart surgery between 2005 and 2010. JET patients were compared with an age matched control group undergoing open heart surgery without JET regarding potential risk factors and outcomes. The overall incidence of JET in infants after open cardiac surgery was 14.3 %. From multivariate analyses, complete repair of tetralogy of Fallot [adjusted odds ratio (AOR) 2.0, 95 % CI 1.12–3.57] and longer aortic cross clamp times (AOR 1.02, 95 % CI 1.01–1.03) increased the risk of developing JET. Patients with JET had longer length of intubation, intensive care unit stays, and total length of hospitalization, and were more likely to require extracorporeal membrane oxygenation support (13 vs. 4.3 %). JET is a common postoperative arrhythmia in infants after open heart operations. Both anatomic substrate and surgical procedure contribute to the overall risk of developing JET. Developing JET is associated with worse clinical outcomes.