Introduction: Right atrial isomerism (RAI), also known as asplenia syndrome, is a severe form of heterotaxy characterized by abnormal thoracoabdominal organ lateralization and complex congenital cardiac malformations. Affected neonates commonly present at birth with cyanosis and respiratory distress and are at increased risk of overwhelming sepsis due to functional or anatomical asplenia. Early recognition is crucial to facilitate prompt cardiac evaluation, infection prophylaxis, and multidisciplinary management. Case Report: A late preterm female neonate (36+1 weeks’ gestation) from a dichorionic diamniotic twin pregnancy presented with persistent respiratory distress, central cyanosis, and a cardiac murmur shortly after birth. Systemic examination was otherwise unremarkable. The infant was admitted to the neonatal intensive care unit for further evaluation and management. Echocardiography demonstrated situs ambiguous with right atrial isomerism, an unbalanced common atrioventricular canal defect, and truncus arteriosus. Abdominal ultrasonography revealed a midline liver, absent spleen, abnormal great vessel orientation, and suspected midgut malrotation. Management included cardiorespiratory stabilization, cardiology consultation, and initiation of antibiotic prophylaxis for asplenia. Discussion: This case emphasizes that neonatal cyanosis unresponsive to oxygen therapy should prompt consideration of heterotaxy syndromes. Early diagnosis of RAI allows timely stabilization, initiation of infection prophylaxis, parental counseling, and coordinated multidisciplinary follow-up to improve outcomes.