Congenital diaphragmatic hernia (CDH) is a congenital anomaly involving the herniation of intra-abdominal contents into the thoracic cavity. Hepatopulmonary fusion (HPF), an exceedingly rare subtype mainly associated with right-sided CDH, presents unique diagnostic and therapeutic challenges. This case report describes a male infant with right-sided CDH complicated by HPF. The intricate anatomical anomaly involved the fusion of the right lung to the liver, posing challenges during surgical separation. The patient experienced postoperative complications, including prolonged ventilation, tracheostomy and pulmonary issues, which led to a prolonged hospital stay. Intraoperative challenges stem from the absence of demarcation between lung and liver tissues and abnormal vascular structures. In summary, managing HPF in right-sided CDH necessitates a customised, multidisciplinary approach to optimise patient outcomes, highlighting the need for ongoing research to refine understanding and treatment strategies.