A 33-year-old female presented with a rare case of fungal meningitis caused by Aspergillus detected for the first time at 15 years after onset. The meningitis repeatedly occurred over a period of 15 years. On admission, cerebrospinal fluid examination found cell count 1340/high-power field, protein 158 mg/dl, and sugar 8 mg/dl, indicating meningitis, although no bacterial or fungal species were detected. Cerebral computed tomography demonstrated hydrocephalus and cervical computed tomography demonstrated a mass lesion on the ventral side of the spinal cord from C4 to C6. Fungal meningitis was suspected and treated with amphotericin B. Her symptoms improved and she was eventually discharged. She was readmitted for recurrence of meningitis and hydrocephalus 2 months later. Amphotericin B was administered and a ventriculoperitoneal (VP) shunt was placed. Shunt malfunction recurred seven times. Aspergillus was detected for the first time from the atrium side of the ventriculoatrial shunt tube at 15 years after onset. Fluconazole was administered. She had narrowing of the cisterna magna, and underwent foramen magnum decompression. The VP shunt was finally reconstructed. Fluconazole administration was continued. Combination of foramen magnum decompression and long-term administration of fluconazole was effective in this case.