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We report a case of other iatrogenic immunodeficiency-associated lymphoproliferative disorders simultaneously arising in the gingiva and intestinal mucosa that required emergency surgery for intestinal perforation, but was finally diagnosed as methotrexate (MTX)-associated lymphoproliferative disorder (MTX-LPD) because they disappeared with MTX withdrawal. An 80-year-old woman was prescribed MTX and prednisolone for rheumatoid arthritis and bisphosphonate for osteoporosis. She was referred to our hospital because of poor wound healing after extraction of the maxillary right first molar. We diagnosed medication-related osteonecrosis of the jaw, as the lesion showed bone exposure, with mild redness and swelling of the gingiva, and the cytological result was Class II. However, 9 months later, following the exfoliation of a partial sequestrum of the maxillary right first molar, a rapidly growing mass with gingival necrosis appeared, necessitating a biopsy. Simultaneously, her abdominal pain worsened and computed tomography showed intestinal perforation; emergency laparotomy was performed to remove the perforation and surrounding ulcer-prone area. Histopathological examination of both lesions revealed diffuse large B-cell lymphomas. The final diagnosis was MTX-LPD, as the mass, gingival necrosis, and remaining small intestinal ulcer disappeared 2 months after MTX discontinuation. The exposed bone completely disappeared after 24 months. There was no evidence of recurrence 60 months after MTX discontinuation. Although intestinal perforation due to MTX-LPD is an extremely rare condition, patients with RA are in an immunosuppressed state. Therefore, MTX-LPD must be recognized as a dangerous condition that requires careful general monitoring.