BackgroundPrimary intramedullary spinal cord lymphoma (PISCL) is rare and easily misdiagnosed with the lack of typical clinical features and non-specific imaging manifestations.Case presentationA 49-year-old man was admitted to our hospital because of persistent limbs numbness, pinprick-like pain in the posterior neck and unsteady gaits. He has brisk tendon reflexes and positive Babinski’s sign. Magnetic resonance imaging (MRI) of the cervical spine showed an abnormal signal with aberrant reinforcement at medulla oblongata and the level of C1-C7. He was clinically diagnosed as longitudinally extensive transverse myelitis (antibody-negative). Steroid pulse therapy was administered and resulted in reduced symptoms. One month later, his situation was exacerbated compared to the onset. We launched a new cascade of steroid pulse therapy. But it did not improve his symptoms. Finally, the biopsy pathology confirmed PISCL. Chemotherapy, radiotherapy and zanubrutinib were administered and until now about 3 years into treatment the patient is still survival.ConclusionsBased on our case and literature review, we recommend that spinal onset patients react ineffectively to standard immunoglobulins or hormonal treatments or experience a relapse after a short time relief should take PISCL into consideration.