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Abstract Background True primary enterolithiasis is an uncommon condition, and nontraumatic perforation of the small intestine (NTPSI) is also an unusual entity. Therefore, NTPSI due to true primary enteroliths is an exceptionally rare complication. Moreover, enterolithiasis and radiation enteritis are also unique combinations. Herein, we present an exceedingly rare case of NTPSI induced by multiple true primary enteroliths associated with radiation enteritis. Case presentation A 92-year-old woman with acute abdominal pain was transferred to our hospital because a computed tomography (CT) scan performed by her family doctor revealed free air and fluid collection within her abdomen. Our initial diagnosis was upper gastrointestinal perforation, and we selected nonoperative management (NOM) with adnominal drainage. Although her general condition was stable, jejunal juice was drained continuously. Given that the CT performed 10 days after onset demonstrated perforation of the small intestine and adjacent concretion, we performed an emergency partial resection of the small intestine and jejunostomy. The resected bowel was 1 m in length and had many strictures that contained multiple enteroliths in their proximal lumens. The patient’s postoperative course was uneventful. The enteroliths were composed of deoxycholic acid (DCA). She was diagnosed with peritonitis due to NTPSI derived from multiple true primary enteroliths associated with radiation enteritis, as she had previously undergone hysterectomy and subsequent internal radiation therapy. Conclusions Clinicians should consider the rare entity of true primary enteroliths associated with radiation enteritis in NTPSI cases with unknown etiologies.