Neonatal thrombotic microangiopathy (TMA) is a rare and severe disease characterized by a triad of non-immune hemolytic anemia, thrombocytopenia, and organ dysfunction in neonates. We describe herein an early-term infant who underwent hemicolectomy at 4 days of age due to intestinal perforation. Following surgery, the patient had recurrent bouts of vomiting and abdominal distention, together with acute kidney injury, non-immune hemolytic anemia, and severe thrombocytopenia. Low complement levels raised the possibility of complement-mediated neonatal TMA. Finally, genetic tests identified a heterozygous mutation in the complement factor I gene. Anti-C5 monoclonal antibody therapy led to complete cessation of the hematological and renal manifestations, but symptoms of intestinal obstruction recurred. Intestinal biopsy demonstrated aganglionosis, compatible with Hirschsprung disease. This presentation is the first known case of neonatal complement-mediated TMA associated with Hirschsprung disease. Moreover, it highlights the importance of considering a diagnosis of TMA in cases of atypical neonatal infectious presentation.