Introduction: We aimed to describe the epidemiological, clinical, laboratory characteristics, and outcomes of central nervous system (CNS) mycosis in patients with human immunodeficiency virus (HIV) and to determine characteristics associated with a higher risk of death. Retrospective data from 77 case histories of HIV-infected patients with neurological symptoms caused by various fungi including Candida and Cryptococcus in Dnipro, Ukraine, were analysed as a case-control study with 40 deceased individuals considered as cases and 37 patients with favourable outcome (survivors) considered as controls. Material and methods: Fungi in cerebrospinal fluid (CSF) were detected with traditional culture methods. Multivariate analysis used (1) binary logistic regression with survivor/dead as a dependent variable and (2) a classification and regression tree (CRT method). Results: A combination of fungal infection with other infections of CNS (dual and triple coinfection) was diagnosed in most cases (n = 53, 68.8%), while the proportion of co-infection was somewhat lower among survivors (59.5%). Clinical manifestations were non-specific. Risk of death was higher among those with tuberculosis (AOR = 2.7, 95% CI: 1.0-7.5) and lower among those infected with Epstein-Barr virus (EBV) (AOR = 0.3, 95% CI: 0.1-1.0) and among patients on ART (AOR = 0.2, 95% CI: 0.1-0.8). Risk of death significantly decreased over time. The classification tree shows that among HIV-mycosis neurological patients not on ART with tuberculosis, the risk of death constituted 75%, while among patients on ART with EBV-infection, all patients survived. Conclusions: Opportunistic mycoses remain an important clinical challenge among immuno-compromised patients especially those who were diagnosed with HIV late, failed to get antiretroviral therapy, and developed tuberculosis.