A term infant who failed to pass meconium and developed bilious emesis on the first day of life underwent a suction rectal biopsy, which revealed the absence of ganglion cells consistent with Hirschsprung’s disease. His final postoperative pathology report indicated an absence of ganglion cells in the anorectal mucosa but some eosinophils in the myenteric plexus and surrounding smooth muscle of the transition zone, aganglionic sigmoid colon, and rectum. These findings are consistent with diagnosis of eosinophilic myenteric ganglionitis. At 6 months old, he had a Soave endorectal pull-through with resection. He had significant, prolonged explosive diarrhea leading to severe perianal breakdown and weight loss. An amino-acid-based infant formula was trialed, and the diarrhea resolved quickly. Ongoing nutrition counseling was needed because of milk sensitivity. He was prone to constipation, and a high-fiber diet was needed. This case shows how collaboration between the pediatric dietitian and pediatric surgical team can lead to better nutritional outcomes including optimal growth, improved formula tolerance, and decreased gastrointestinal (GI)-related complications after surgery. It also reinforces how long-term follow-up is critical from both a nutrition and surgical standpoint, to address the long-term nutrition issues that can ensue from surgical intervention of Hirschsprung’s disease in infancy. This particular case is especially interesting as the patient is the youngest documented case found in the literature with a case of eosinophilic myenteric ganglionitis occurring with Hirschsprung’s disease.