A 76-year-old woman treated with methotrexate (MTX) for rheumatoid arthritis was urgently transported to our hospital due to hypotension and pancytopenia. MTX-induced pancytopenia was suspected, and MTX withdrawal and folic acid were started. Although the pancytopenia improved, diffuse ground-glass opacification had exacerbated in both lung fields on chest computed tomography. The pathological findings of a transbronchial lung biopsy showed alveolitis with lymphocytic infiltration and granulomas, and polymerase chain reaction (PCR) for Pneumocystis jirovecii from bronchoalveolar lavage fluid was negative, leading to a diagnosis of MTX pneumonia. Her pulmonary opacification improved markedly with steroid treatment. The clinical course, which became apparent with the improvement of pancytopenia, suggested the involvement of immune reconstitution inflammatory syndrome as the mechanism of MTX pneumonia in this case.