Thrombosis, especially thrombosis of the pulmonary artery, is a large contributor to morbidity and mortality following comprehensive stage 2 procedure for single ventricle cardiac physiology. A peri-operative management protocol was implemented at our institution in March 2010. It includes 6 weeks of therapeutic anticoagulation post-operatively to mitigate the thrombotic risks in this patient population. This is a retrospective study of hospitalized children who received post-operative anticoagulation following a comprehensive stage 2 procedure for single ventricle cardiac physiology at a free-standing children’s hospital. The primary objectives are to describe our institution’s anticoagulation strategy and report on the number of thromboses and major bleeding episodes in the 6 weeks post-operatively. Secondary objectives include the dose of enoxaparin required to obtain a therapeutic low-molecular weight anti-factor-Xa (AFXaLMWH) level, and the number of patients outside of the therapeutic range. A total of 71 infants were included in the final analysis. Four patients experienced a thrombosis episode and three patients experienced clinically significant bleeding. The mean dose of enoxaparin required to obtain a therapeutic AFXaLMWH level between 0.5–1 unit/mL was 1.23 mg/kg SQ every 12 h and 37% of patients achieved goal AFXaLMWH levels with the initial starting dose of enoxaparin 1 mg/kg SQ every 12 h. We describe a 9-year experience of anticoagulation after single ventricle palliation. Anticoagulation with therapeutic AFXaLMWH goals of 0.5–1 unit/mL may reduce the rates of clinically significant thrombosis post-operatively in this population and appears safe without increase in significant bleeding episodes when compared to a historical cohort. Further studies comparing this population to those who do not receive post-operative anticoagulation are warranted.