A malignant peripheral nerve sheath tumor (MPNST) is a rare neoplasm arising from peripheral nerve sheath. Here, we report the first case of MPNST arising in the colon and also the youngest case of MPNST in the gastrointestinal tract. The patient was a 2-day-old neonate with symptoms and signs of intestinal obstruction. The patient had no family history or stigmata of neurofibromatosis type 1. A computed tomographic scan revealed a 5-cm-sized mass in ascending colon causing intestinal obstruction, and emergent right hemicolectomy was performed. The microscopic examination showed atypical spindle cells with hyperchromatic nuclei and high mitotic activity. The results of immunohistochemical staining, which showed positivity for S-100 and vimentin as well as negativity for smooth muscle actin, CD34, and c-Kit, supported the final diagnosis of MPNST. Genetic analysis of the patient revealed no abnormalities. After surgery, the patient recovered uneventfully and has been free of the disease for 17 months.