Pediatric intestinal perforation is a surgical emergency that must be promptly addressed regardless of the specific cause. Here we report a case of colon perforation caused by indeterminate inflammatory bowel disease (IBD) in an autistic 13-year-old boy. Ulcerative colitis (UC) and lymphoma were first suspected but subsequently ruled out. The patient was previously hospitalized locally for 8 days due to diarrhea. He was diagnosed with UC and colon perforation in the emergency room. He then underwent subtotal colectomy with end ileostomy. Pathological examination of the colon showed multiple perforations with absence of chronic crypt change (a characteristic of UC), presence of undermining ulcers, and atypical lymphocyte infiltrations. Lymphoma was ruled out from immunohistochemistry and blood tests. Indeterminate colitis was finally suggested as the cause of perforation. Genetic analysis confirmed KBG syndrome, but no abnormalities otherwise known to be relevant to colitis. This case demonstrates that spontaneous colon perforation might occur in KBG syndrome patients suffering from severe enteritis without IBD, malignancy, or other conditions known to cause perforation, supporting the necessity of close monitoring when such patients present with severe symptoms including fever and abdominal distension without showing improvement.