Primary cardiac tumors are very rare in children. Rhabdomyoma is the most common benign tumor in fetuses and neonates. Most cases do not require any surgical intervention due to absence of clinical symptoms and a high rate of spontaneous regression within the first year of life. However, some neonates can have significant abnormalities of intracardial hemodynamics related to the obstruction of the left and right ventricle outflows; this is an indication to emergency surgery. As a rule, complete or partial resection of the tumor mass provides uneventful postoperative course and is not associated with a relapse of rhabdomyoma in the long-term.We present a clinical case of a 15-days old neonate who underwent an emergency surgery due to advanced tumor obstruction of the blood flow in the right ventricle outflow tract (RVOT). At preoperative echocardiography, there was a pulmonary artery systolic pressure gradient of 90 mm Hg. Moderate hypoxemia (SaO2 90%), breathing rate of up to 55 per minute, together with echocardiographic results, indicated the impaired pulmonary blood flow and the need for the tumor resection. The tumor was completely resected through the right ventricle access with cardiopulmonary bypass and cardioplegia, with subsequent autologous pericardium patching of the right ventricle. The postoperative period was uneventful; the patient was extubated at day 2 and discharged at day 11 after surgery. The diagnosis of rhabdomyoma was confirmed histologically. At one month after surgery, no additional tumor masses were found in the heart chambers and septum.Rhabdomyoma causing severe obstruction of the RVOT in a newborn is a rare life-threatening complication of the natural course of benign heart tumors in children. The presence of dyspnea at rest, moderate desaturation, and echocardiographic data determined the rejection of the conservative management commonly adopted in most cases of cardiac rhabdomyomas, and were indications for an emergency surgery. In the long-term postoperative period, magnetic resonance imaging should be done to exclude tuberous sclerosis.