Introduction: The coexistence of visceral myopathy (VM) and Hirschsprung's disease (HD) is exceptionally rare yet clinically significant. Both conditions necessitate full-thickness biopsy for precise diagnosis. Despite potential similarities in presentation, no documented cases have established an association between these two disorders. Case presentation: We present a 3150-g, full-term male newborn, four days old, born without maternal pathologies or antenatal diagnoses. He was admitted to the emergency department with one day of fecal vomiting, lethargy, and decreased intake. On admission, he exhibited hypothermia, tachycardia, and his oxygen saturation was 94%. Physical examination revealed a septic, dehydrated, poorly perfused newborn with a distended abdomen and absent bowel sounds. Abdominal X-ray indicated pneumoperitoneum. Emergency laparotomy revealed colonic perforation necessitating resection and colonic anastomosis, with the abdomen left open and covered by a dressing, followed by a loop-ileostomy in the subsequent surgery. Surgical biopsies, including a later laparoscopic intestinal mapping, confirmed VM and HD. The patient progressed with complete oral feeding, normal bowel transit through the ileostomy, and no associated complications. Currently, the patient awaits resection of the aganglionic segment and rectal pull-through. Conclusion: This case may suggest either an incidental finding or an undiscovered common etiology linking HD and VM in neonatal intestinal perforation. Comprehensive diagnostic approaches, personalized treatments, and further exploration of their genetic and developmental connections are crucial for improving patient outcomes.