Pompe disease is a hereditary lysosomal storage disorder characterized by a deficiency in the acid alpha-glucosidase (GAA) enzyme, leading to glycogen accumulation in muscle and neurons. Clinical manifestations vary from severe infantile-onset with hypertrophic cardiomyopathy and early mortality due to respiratory insufficiency to late-onset with proximal muscle weakness, gross motor delay, and progressive respiratory insufficiency. A case of an 11-year-old boy who reported to the pediatric emergency department with a nine-year history of progressive muscle weakness and a one-month history of anemia symptoms (easy fatigue, shortness of breath, pale appearance) and heart failure (orthopnea, dyspnea). His family history included consanguineous marriages and similar conditions in his brother and maternal uncle. On examination, he appeared pale, malnourished, and exhibited signs of respiratory distress and tachypnea. His cardiovascular examination revealed apex beat displacement, elevated JVP, bilateral pedal edema, mild ascites, positive hepatojugular reflux, and systolic murmurs. Respiratory examination indicated bilateral crepitation and wheezes. Musculoskeletal examination showed decreased muscle mass and power, especially in proximal muscles. Abdominal examination revealed hepatosplenomegaly and mild ascites. Radiological findings included an enlarged cardiac shadow with pleural effusion and bilateral radio-opaque shadows on chest x-ray, while echocardiography showed impaired left ventricular systolic function with mild to moderate mitral and tricuspid regurgitation. Laboratory tests indicated elevated aspartate aminotransferase, LDH, and creatine kinase levels, along with normocytic, normochromic anemia. Muscle biopsy from the hamstring revealed PAS stain positive granules. These clinical, radiological, and laboratory findings strongly suggest late-onset Pompe disease, marking this as potentially the second reported case in Pakistan.