A 69-year-old male who had been treated with methotrexate (MXT) for 4 years due to rheumatoid arthritis (RA) was admitted to our hospital for dyspnea and fever. He had swelling of the parotid gland and pharyngeal mass, and his chest CT showed diffuse fine miliary shadows and subpleural nodular shadows. The finding of granulomas and organization in the alveolar space revealed by transbronchial lung biopsy indicated a diagnosis of MTX pneumonia. Moreover, the finding of invasion of mixed polyclonal lymphoid cells and EBER-1-positive large cells by pharyngeal biopsy suggested lymphoproliferative disorder (LPD). Both pulmonary and pharyngeal lesions improved together only on MTX withdrawal. In this case, MTX pneumonia and MTX-LPD, which has been considered to have a different etiology developed simultaneously; further elucidation is required for the mechanism of action of MTX.