Hirschsprung's disease is a congenital condition characterized by the absence of ganglion cells in the intestines, leading to bowel obstruction. The lack of ganglion cells disrupts the normal motility of the intestines, causing a functional obstruction. This can lead to enterocolitis, an inflammation of the intestines, which is a serious complication in infants with Hirschsprung's disease. This case report follows a male infant with multiple admissions for recurrent enterocolitis secondary to undiagnosed Hirschsprung's disease with unresolving diarrhea. This study underscores the significance of early diagnosis and management, even in cases of atypical presentation, emphasizing the role of antibiotics, bowel decompression, and surgical intervention. The findings highlight the complexity of managing Hirschsprung's disease and offer insights into tailored approaches for optimizing patient outcomes.