Background: Inflammatory myofibroblastic tumor (IMT), an infrequent mesenchymal lesion composed of myofibroblastic and fibroblastic spindle cells with inflammatory infiltration, mostly occurred in pediatric patients. IMT has been reported in a number of locations throughout the body. However, the cases occurred in the gastrointestinal tract, especially those involving the sigmoid colon in pediatric patients, are very rare and even have not been reported. Here we present a case of a large IMT originating from the sigmoid colon and invading the omentum and the surrounding tissues in an 11-month-old boy. Case presentation: The patient is an 11-month-old boy initially presenting with symptoms of fever and vomiting. Abdominal ultrasound revealed an inhomogeneous echo with a size of 9.9*4.6 cm in the left lower abdomen. Abdomen computed tomography (CT) scanning confirmed that a mass with a size of 10*8*6 cm located in the left middle and lower abdomen. Post-operative pathological examination confirmed the histopathologic diagnosis of IMT. Complete resection of the tumor along with the involved colon segments were performed and followed by end-to-end colon anastomosis. The boy recovered well without postoperative complications or recurrence during one-year follow-up. Conclusions: Colon IMT is extremely rare; its etiology and pathogeny are unclear. Imaging examination may provide reliable evidence for determining IMT. However, postoperative histopathologic examination is also important for the final diagnosis. Complete tumor excision, accompanied by rare recurrence and satisfying survival, is the best therapeutic approach at present. This case report may complete the clinical presentation of IMT by reminding physicians not to ignore the possibility of IMT in the colon.