Lymphatic malformations frequently present as benign masses in the neck and clavicle region among infants and young children. Cystic hygroma represents an often-encountered form of lymphatic malformation. This case report details the medical history of a one-year-old girl characterized by a multifaceted medical background, initially exhibiting symptoms of persistent cough, cold, and neck swelling. Further investigations revealed more severe conditions: complex congenital heart defects, including large atrial septal defect (ASD), large ventricular septal defect (VSD), and aorta arising from the right ventricle with cystic hygroma and annular pancreas. The patient underwent various diagnostic tests, including chest X-rays, ultrasound, magnetic resonance imaging (MRI), and computed tomography pulmonary angiogram (CTPA), leading to multidisciplinary treatment involving sclerotherapy for cystic hygroma and supportive therapies. The case underscores the challenges in diagnosing and managing pediatric patients with overlapping conditions and the critical need for continuous follow-up.