We examined the efficacy of liposomal amphotericin B (L-AMB) for intractable cryptococcal meningoencephalitis in a patient with acquired immunodeficiency syndrome (AIDS) and the presence of immune reconstitution syndrome (IRS) caused by the treatment. A 34-year-old patient presented with meningitis. Cryptococcal organisms were detected microscopically in the cerebrospinal fluid (CSF) with Indian ink staining, and were then cultured from the CSF. Initial treatment with amphotericin B and flucytosine (5-FC) or voriconazole and/or fluconazole failed to eradicate cryptococcal organisms from the CSF. Secondary treatment with L-AMB and 5-FC following seven months of antiretroviral therapy was successful. Simultaneously, treatment with L-AMB caused severe brain edema likely due to IRS. There were large differences in immune function improvement and liposomalization of the fungicide between the initial and secondary treatments. In conclusion, differences in immune status should be considered when administering L-AMB, in order to prevent IRS-related complications.