Invasive aspergillosis has an extremely high mortality rate. In Japan, micafungin, an echinocandin drug that has a new mechanism of action as an antifungal agent and has a clinical effect against Aspergillus species, became available in 2002. However, little is known about its penetration into the central nervous system (CNS), or its efficacy for the treatment of invasive CNS aspergillosis. We report a 65-y-old female with diabetes mellitus and CNS aspergillosis who was treated with micafungin. During treatment, micafungin concentrations were measured in the cerebrospinal fluid and plasma. On a dose of 300 mg/d, the ratio of the micafungin concentration in the cerebrospinal fluid to that in plasma was extremely low (0.2%-0.05%); nevertheless, the patient did not have a relapse of invasive CNS aspergillosis after micafungin treatment.