Spinal cord biopsy is a difficult procedure fraught with the risk of false-negative results or even misdiagnosis in up to 30% of cases. Differential diagnoses of spinal cord lesions include a wide range of inflammatory, infectious and neoplastic diseases. Given the importance of correctly managing these pathologies, it is crucial to avoid delays in making the correct diagnosis in order to improve the patient's outcome. We present here the case of a 21-year-old male with rapidly progressing sphincter and lower limb motor dysfunctions up to complete paraplegia with evidence of thoracic spinal cord lesion on magnetic resonance imaging. None of the blood and cerebrospinal fluid tests pointed to a diagnosis, while a first spinal cord biopsy revealed an inflammatory necrotic process. After several weeks of empirical treatments and clinical stability, the patient started having focal structural seizures that became generalized with local progression of the lesion and diffuse leptomeningeal spread on magnetic resonance imaging. A second spinal cord biopsy found a grade IV glioblastoma with H3 K27M histone mutation. Unfortunately the patient passed away before any treatment could be initiated. In this report, the authors analyze the difficulty of making the rapid, correct diagnosis of a highly malignant intrinsic spinal cord lesion, discussing also possible strategies to avoid diagnostic delays and to improve the outcome of these difficult patients.