Background: Mucopolysaccharidoses (MPS) are rare, metabolic lysosomal storage disorders caused by the deficiency of enzymes required for the stepwise breakdown of glycosaminoglycans (GAGs). We report a case that was discovered to be Mucopolysaccharidosis Type II and was presented to the hospital with signs and symptoms of congenital diaphragmatic hernia. The hernia was repaired, and the patient was discharged on BiPAP and High-flow Oxygen. Case Presentation: A vaginally delivered male child was presented to the hospital with a fever, cough, and shortness of breath. He has a history of recurrent chest infections treated as pneumonia. The child was born to a mother with a pregnancy complicated with gestational diabetes and the presence of polyhydramnios. Screening tests during the pregnancy reported no congenital anomalies. The patient was admitted, and a chest X-ray was performed and revealed cardiomegaly, pulmonary infiltrates consistent with pneumonia and bowel herniation noted through the right hemidiaphragm. A Computed Tomography (CT) scan of the thorax and Barium swallow was done, and Pneumonia and Congenital diaphragmatic hernia was confirmed. Genetic testing was done because the patient has coarse facial features, developmental delay, hypotonia and skeletal abnormalities. Iduronate-2-sulfatase enzyme levels were significantly low, all the other enzymes were normal in range, and the diagnosis of Type II Mucopolysaccharidosis was established. The patient was stabilized and operated on for diaphragmatic hernia repair. No enzyme-replacement therapy (ERT) was given because it is not available in Jordan. He was discharged on high-flow Oxygen and bilevel positive airway pressure (BiPAP). Conclusion: Depending on the typical presentation to suspect Mucopolysaccharidosis is not always the key to diagnose it. MPS is a multi-organ disorder and rare presentations should not be disregarded.