A 76-year-old man who was taking prednisolone and methotrexate for rheumatoid arthritis presented with gastric ulcers. Chest X-ray images showed multiple pulmonary nodules. Transbronchial lung biopsy specimens showed lymphocytic infiltrates but no malignant cells. The radiographic findings gradually ameliorated over a month, but then deteriorated 5 months later. We performed video-assisted thoracoscopic biopsy of the left lung, and the biopsy specimens showed lymphocytic infiltration with necrosis, in which the atypical lymphocytes were positive for Epstein-Barr virus-encoded small RNAs in situ hybridization (EBER-ISH). A diagnosis of lymphomatoid granulomatosis was determined. One year before this diagnosis, the patient was found to have an inflammatory liver tumor that had disappeared spontaneously within a month. A new pathological review of the liver and stomach lesions demonstrated EBER-ISH-positive lymphocytes, and therefore we assumed that they were pathological features of lymphomatoid granulomatosis. The chest radiographic findings improved gradually after the discontinuation of methotrexate. We therefore suggest that methotrexate treatment may be associated with the development of lymphomatoid granulomatosis in patients with rheumatoid arthritis. Lymphoproliferative disorders, including lymphomatoid granulomatosis, should be considered in patients with rheumatoid arthritis who are receiving methotrexate.