Cryptococcus (C) neoformans infection mainly occurs in immunocompromised hosts, especially those with AIDS, and skeletal infection is a rare presentation of cryptococcosis. We report a rare case of disseminated cryptococcal infection of the lumbar spine in an immunocompetent man caused by Cryptococcus neoformans var. grubii. The lesion position first appeared on upper right lung and then spread to the fourth lumbar vertebra. The result of periodic acid-Schiff (PAS) and Gomori's methenamine silver (GMS) staining of the tissue sample matched cryptococcal infection, but multiple culture was negative. Eventually, C. neoformans var. grubii was confirmed using next-generation sequencing (NGS). Current follow-up of 12 months indicated a stable condition after antifungal therapy (fluconazole 400 mg/day) combined with surgery. Our case reminds that physicians must consider the possibility of skeletal cryptococcosis in patients with bone lesions, and NGS might be an excellent option to obtain the most accurate diagnosis in clinical practice.