Background Myeloid sarcoma is a rare, extramedullary, solid tumor derived from immature myeloid cell precursors. It is most frequently accompanied by acute myelogenous leukemia, though infrequently found in non-acute myelogenous leukemia patients. The tumor may involve any part of the body, but the lumbar spine is seldom involved. The present case study aims to understand the diagnosis and surgical treatment of a rare primary isolated myeloid sarcoma of the lumbar spine causing aggressive spinal cord compression in a non-acute myelogenous leukemia patient. Case presentation A 29-year-old man complained of an aggressive radiating pain to the lower extremities and moderate dysuria with a Visual Analogue Scale score that gradually increased from 3 to 8. Lumbar enhanced magnetic resonance imaging and computed tomography revealed a lumbar canal lesion at lumbar spine L2 to L4 with spinal cord compression. A whole body bone scan with fused single photon emission computed tomography/computed tomography demonstrated abnormal Tc-99m-methylene diphosphonate accumulation in the L3 lamina and spinous process. No evidence of infection or hematology disease was observed in laboratory tests. Due to rapid progression of the symptoms and lack of a clear diagnosis, decompression surgery was performed immediately. During the operation, an approximately 6.0 x 2.5 x 1.2 cm monolithic, fusiform, soft mass in the epidural space and associated lesion tissues were completely resected. The radiating pain was relieved immediately and the dysuria disappeared within 1 week. Intraoperative pathological frozen section analysis revealed a hematopoietic malignant tumor and postoperative immunohistochemistry examination confirmed the diagnosis of myeloid sarcoma. Conclusions The primary isolated aggressive lumbar myeloid sarcoma is rarely seen, the specific symptoms and related medical history are unclear. Surgery and hematological treatment are effective for understanding and recognizing this rare tumor.