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Introduction: Eosinophilic colitis (EC) is an uncommon inflammatory condition with the lowest reporting rate among eosinophilic gastrointestinal disorders. EC, which is characterized by the accumulation of eosinophilic cells, is typically diagnosed by a combination of clinical, imaging, and microscopic evaluations. We present a rare case of complete colonic obstruction due to eosinophilic colitis (EC) in a neonate, which was successfully managed with surgical intervention. Case presentation: A 27-day-old female neonate presented with bloody diarrhea and anemia, followed by repeated bilious vomiting, feeding intolerance, and abdominal distention along with very limited bowel motion. Abdominal radiography showed contrast-medium retention in the colon with persistent bowel dilatation while a lower GI contrast enema indicated a cut-off sign at the level of the sigmoid colon. Subsequent colonoscopy revealed a rectosigmoid stricture with complete luminal obstruction 7 cm from the anal verge. Histopathological examination showed marked eosinophilic infiltration through all the layers of the colon. Exploratory laparotomy showed a 3-cm complete stricture with severe gross inflammation in the rectosigmoid colon. Resection of the affected segment and primary anastomosis was achieved successfully, and the patient showed an uneventful recovery with no symptoms at discharge as well as age-appropriate weight gain at the one-year follow-up examination. Conclusion: To our knowledge, this is the first reported case of rectosigmoid stricture caused by EC in a neonate, and it highlights the importance of including EC in the differential diagnosis of colonic obstruction in neonates as well as the need for surgical management in such cases.