Pulmonary arterial hypertension is a common complication of uncorrected left-to-right shunt congenital heart disease. Beraprost have been used widely to treat pulmonary arterial hypertension in adult. However, the efficacy of the drug in Indonesian children has not been investigated. This study aim is to evaluate the efficacy of Beraprost in treating pulmonary arterial hypertension related to left-to-right shunt congenital heart disease. A randomized control trial was used in this study between April to September 2017 in Cardiology outpatient clinic of Dr. Soetomo General Hospital. Subjects aged 2-12 years with pulmonary arterial hypertension randomly received Beraprost 0.35 mcg/kg eight hourly for 12 weeks. Efficacy was evaluated by echocardiography and adverse effect was monitored. Data were analysed by statistical software using t-test and Mann Whitney test with significance level set to 0.05. All procedures were approved by hospital ethics committee and registered at the ClinicalTrials.gov. Twenty two children were recruited into the study. Resolution of Beraprost in decreasing pulmonary arterial pressure was -21.32 ± 11.06 mmHg (p=0.034). Adverse effects reported were headache. As conclusion, Beraprost is effective and safe as initial pharmacologic treatment in treating pulmonary arterial hypertension related to left to right shunt congenital heart disease.