Cor triatriatum dexter (CTD) is a very rare cardiac anomaly in which a membrane divides the right atrium (RA) into two chambers. Clinical presentation of CTD is slightly variable. Most patients are asymptomatic, and a lesion is discovered during echocardiography or surgery for other cardiac lesions. When accompanied with interatrial defects, patients with CTD exhibit cyanosis because of the right-to-left shunt via interatrial communication. Moreover, CTD and cyanotic congenital heart diseases require differentiation. To our knowledge, there are no reports of infants with a hypoplastic RV who were diagnosed with CTD, and there is no consistent opinion about the best treatment strategy for CTD. Here, we describe a male neonate with CTD and a hypoplastic RV having symptoms of central cyanosis soon after birth. A large membranous structure was identified in the RA and flow from the inferior vena cava was partially redirected into the left atrium (LA) via the patent foramen ovale (FO). We surgically resected a large membranous structure from the RA and partially closed the FO when the patient was 4 months old. We performed cardiac catheterization 12 months after surgery and confirmed that the RV was well-developed and had good function. We speculate that for CTD with hypoplastic RV and inter-atrial communication, resection of the Eustachian valve and partial closure of the FO may be effective treatment strategies as long as the size of the RV is considered. Further studies on RV size and intervention for the FO in such cases of CTD are needed.