Pulmonary arterial hypertension (PAH) related to left-to-right shunt can progress to Eisenmenger syndrome, a serious and fatal disease that is not yet curable. This pilot study considered stem cell injection as a new treatment modality in persistent pulmonary hypertension after the correction of a congenital heart defect. Three patients with persistent pulmonary hypertension after ventricular septal defect repair were included in this pilot study for a clinical trial. Mononuclear stem cells derived from patients’ bone marrow specimens were injected into the right and left pulmonary arteries via cardiac catheterization. The patients were followed over a 6-month period, with six-minute walk test, echocardiography and repeated angiography performed in the sixth month after treatment. The results of the study showed improvement of 40 m, 280 m and 100 m in 6-minute walk distance in patients 1 to 3, respectively. The peak PR gradient decreased 2, 5 and 9 mmHg by echocardiography, and mean PA pressure decreased 21, 22 and 9 mmHg by catheterization in patients 1 to 3, respectively. Pulmonary artery resistance decreased 4, 4.5 and 1.3 Wood units after 6 months of stem cell therapy in the three patients. No short-term complications were detected in this pilot trial, and all patients tolerated the procedure without any complications. Intrapulmonary artery injection of stem cells may have a role in the treatment of persistent PAH secondary to congenital heart disease. This procedure is feasible, with no significant complications, and this study can be considered as a platform for larger studies.