Undifferentiated neoplasms of unknown primary sites are rare. It is difficult to identify their characteristics and determine the appropriate chemotherapy regimen to be used. Undifferentiated/rhabdoid carcinoma is reportedly associated with loss of SWI/SNF chromatin remodeling complexes, such as observed in SMARCA4-deficient tumors. However, little is known about SMARCA2/BRM-deficient tumors. A 48-year-old man presented with low back pain. Computed tomography (CT) revealed intraperitoneal lymph nodes and multiple bone metastases that invaded the thoracic and lumbar spinal canals. The primary tumor was not identified despite the standard diagnostic methods being used. CT-guided needle biopsy of right iliac bone metastasis showed that the tumor had an undifferentiated/rhabdoid morphology. Immunostaining revealed that the tumor was SMARCA2/BRM-deficient despite both SMARCB1/INI1 and SMARCA4/BRG being retained. We found no genomic alterations during domestic next-generation sequencing panel profiling, which can identify 114 genes. Thus, he was diagnosed with SMARCA2/BRM-deficient undifferentiated/rhabdoid carcinoma of an unknown primary site with multiple bone metastases and intraperitoneal lymph node metastasis. We administered radiotherapy to the thoracic and lumbar spine to improve cord compression, and carboplatin (CBDCA) and paclitaxel regimen was chosen as first-line chemotherapy, but this was discontinued due to an anaphylactic shock. We then selected the CBDCA and gemcitabine regimens; however, the patient did not continuously receive the regimen due to myelosuppression. Radiation therapy effectively relieves pain and cord compression. To our knowledge, this is the first reported case of SMARCA2/BRM-deficient undifferentiated/rhabdoid carcinoma of an unknown primary site. Further studies are needed to improve SWI/SNF-deficient tumor identification methods.