Background The inappropriate use of systemic antifungal agents can result in unnecessary exposure, adverse events, increased microbial resistance and increased costs. Aim This study analysed the use of systemic antifungal agents and adherence to treatment guidelines for fungal infections. Setting A Brazilian tertiary hospital. Methods This cross-sectional study investigated 183 patients who were treated with systemic antifungals. Antifungal drugs were classified according to the fourth level of the Anatomical Therapeutic Chemical classification system. The appropriateness of treatments was analysed with respect to the indication, dose and potential drug-drug interactions. Descriptive and univariate statistical analyses were performed. The main outcome measure was the frequency of adherence to treatment guidelines for fungal infections. Results The number of established treatments was 320, with 163 (50.9 %) pre-emptive, 63 (19.7 %) targeted, 56 (17.5 %) empirical and 38 (11.9 %) prophylactic treatments. The overall adherence to the treatment guidelines was 29.4 %. The proportion of appropriate treatment considering indication, dosage and drug-drug interactions was 84.1, 67.8 and 47.2 %, respectively. The most commonly prescribed systemic antifungal agents were fluconazole in 170 (53.1 %), voriconazole in 43 (13.4 %) and amphotericin B deoxycholate in 36 (11.3 %) cases. Conclusion The study showed a low proportion of appropriate antifungal drug use; the dosage and drug-drug interactions criteria were the determining factors for the high percentage of non-adherence to treatment guidelines in the hospital. The profile of antifungal agents used showed the predominance of fluconazole as well as the use of new antifungal drugs.