We present a case of thoracic SMARCA4-deficient undifferentiated tumor that needed to be differentiated from malignant lymphoma owing to multiple lymph node swelling and marrow involvement. A 52-year-old man developed multiple lymphadenopathies along with anorexia, general fatigue, fever, and sweating 2 months prior to admission. F-fluorodeoxyglucose positron emission tomography/computed tomography (PET/CT) scan revealed a mass lesion on the right upper lung, generalized lymph node swelling, and bone metastasis, indicating the presence of suspicious lung cancer; therefore, he was referred to our hospital. Malignant lymphoma was suspected at the time of admission because of elevated levels of lactate dehydrogenase (11,977 U/l) and soluble interleukin 2 receptor (2,152 U/ml) as well as marrow infiltration of large abnormal cells. On day 11, the patient died from rapid respiratory failure. Histological and immunohistochemical features of the pleural effusion cell block led to the diagnosis of thoracic SMARCA4-deficient undifferentiated tumor. Thoracic SMARCA4-deficient undifferentiated tumor was recently introduced in the 2021 World Health Organization classification of lung tumors, with most patients being young adults with a history of heavy smoking and poor prognosis. Because of the multiple lymph node swelling and marrow involvement, this undifferentiated tumor should be distinguished from malignant lymphoma.