Background Scimitar syndrome is a rare form of partial anomalous pulmonary venous drainage associated with pulmonary hypertension and congestive heart failure that may lead to death in the newborn infant. Although it is described with anomalies of the lung, heart and their vascular structure, extremely rare association with imperforate anus had been reported. The third case of Scimitar syndrome and imperforate anus will be reported in this case report. Case presentation A 3 days old male neonate with imperforate anus presented with abdominal distention. Loop colostomy was done to relieve abdominal distension. The chest x-ray revealed a curved shadow on the right mid lung zone extending to the diaphragm abutting and indenting the inferior vena cava (scimitar sign). Abdominal ultrasound, transthoracic echocardiography and computerized tomographic angiography confirmed the presence of Scimitar vein and associated dextro-position of the heart, hypoplastic right lung, hypoplastic right pulmonary artery, secundum atrial septal defect with bidirectional shunt, patent ductus arteriosus, pulmonary hypertension, left superior vena cava, and systemic collateral arteries feeding the lower lobe of the right lung. The rare association of scimitar syndrome with imperforate anus is discussed. Conclusion Scimitar syndrome associated with imperforate anus with and without VACTERL association has been reported previously only in four cases. The knowledge of association between imperforate anus and Scimitar syndrome helps for early detection and management of cases. It is recommended to have high index of suspicion in every newborn with imperforate anus to check for symptoms of dextro-position of the heart, right lung hypoplasia which may be indicate scimitar syndrome. Electronic supplementary material The online version of this article (10.1186/s12887-019-1643-z) contains supplementary material, which is available to authorized users.