Clostridium septicum is a very rare cause of severe spontaneous pediatric enterocolitis and is often associated with underlying malignancy or immunocompromise. Likewise, cyclic neutropenia is a rare congenital immunodeficiency that is characterized by cyclical periods of neutropenia, often with more severe symptoms in the pediatric population. Here, we present a unique case of spontaneous C. septicum enterocolitis, sepsis, and myonecrosis in a child with undiagnosed cyclic neutropenia. Early recognition of pediatric sepsis, frequent reevaluation and identification of rapidly progressive infection, and early surgical intervention are critical for the effective management of a rare and severe infection.