Early detection and diagnosis of  pneumonia (PCP) among non-HIV patients is crucial because of its rapid course. However, when PCP is suspected due to respiratory symptoms in pancytopenia patients, performing bronchoalveolar lavage is often challenging because of progressing respiratory failure and elevated risk of bleeding. We report the case of a 78-year-old woman with rheumatoid arthritis who developed PCP during methotrexate (MTX)-induced pancytopenia. One week before hospital admission, she presented with fever and malaise without respiratory symptoms. We made a definitive diagnosis via Grocott-stained sputum with reference to her elevated plasma β-D-glucan. Respiratory failure was already advanced at diagnosis, and the patient died on hospital day 11. Because MTX use and MTX-induced pancytopenia increase the risk of PCP, fever during pancytopenia may indicate the need for plasma β-D-glucan and high-resolution computed tomography for its early detection and treatment, even without respiratory symptoms. Minimally invasive techniques such as Grocott-stained sputum or real-time polymerase chain reaction (PCR) of sputum may be helpful in diagnosis when bronchoscopy is not feasible due to pancytopenia.