Infantile-onset Pompe disease manifests with early signs of cardiomyopathy during the first few days to weeks of life. We present the case of a newborn born via emergency cesarean section with atrial flutter and moderate biventricular hypertrophy who was diagnosed with Pompe disease on New York State newborn screen. Diagnosis was confirmed with repeat leukocyte acid alpha-glucosidase (GAA) enzyme activity, GAA gene sequencing, urine Hex4, and evaluation of Cross-Reactive Immunological Material (CRIM) status. The patient was also found to be persistently neutropenic which to our knowledge has not been previously reported in the literature in association with Pompe disease. This report highlights the impact that newborn screening had on time to diagnosis and initiation of treatment with enzyme replacement therapy. We also discuss how our patient's concurrent neutropenia impacted decision making related to immune tolerance induction prior to starting enzyme replacement therapy.