Abstract Background Double chambered right ventricle is a rare congenital heart disease that is characterised by the presence of an anomalous muscle bundle that divides the right ventricle into a low pressure superior (distal) chamber and a high pressure inferior (proximal) chamber. It is found in association with a ventricular septal defect in 90% cases with other associations being tetralogy of Fallot, transposition of great vessels, atrial septal defect and Ebstein’s anomaly. On the other hand, subaortic membrane is a form of discrete subaortic stenosis that is characterised by a membranous diaphragm in the subvalvular location of the left ventricular outflow tract. Both of these entities are responsible for causing subvalvular outflow tract obstruction. The occurrence of double chambered right ventricle in association with subaortic membrane is an extremely rare entity with only a few case reports available in the literature. Case report A 13-year-old male child with history of chest pain and palpitations presented to the outpatient department of a tertiary care center. Transthoracic echocardiography revealed a subaortic membrane producing a pressure gradient across the left ventricular outflow tract with dilatation of the right atrium and right ventricle which could not be fully evaluated on echocardiography. Cardiac computed tomography was then performed which additionally revealed an anomalous muscle bundle coursing across the right ventricle from the septum to the subinfundibular region creating a double chambered right ventricle. The patient was then taken up for reconstruction of right ventricular outflow tract and resection of subaortic membrane. Conclusion Right and left outflow tract obstructions are rare congenital lesions which when seen in combination, become even more infrequent. Echocardiography is a robust tool that detects turbulent flow to identify such lesions. However, poor acoustic window may sometimes result in missing these lesions and computed tomography in such situations can play an important role in detection as well as complete preoperative imaging evaluation.