We herein report a case of methotrexate‐associated lymphoproliferative disorder (MTX‐LPD) showing fibrin‐associated large B‐cell lymphoma‐like heart valve lesions, and Epstein‐Barr virus (EBV)‐positive mucocutaneous ulcer‐like cutaneous and oral mucosal lesions. MTX‐LPD is a critical complication that can occur in RA patients who are treated with MTX. EBV also plays a defining or important role in LPDs. Among the sites of MTX‐LPD, 40−50% occur in extranodal sites, including the gastrointestinal tract, skin, liver, lung, and kidney. There are few reports of MTX‐LPDs involving the heart valves, and to the best of our knowledge, this is the first case to be reported in the English literature. The possibility of EBV‐positive LPD should be considered in RA patients, even in patients with an atypical site, as in this case.