Abstract Objectives The direct cost of invasive fungal disease (IFD) includes antifungal drugs as well as diagnostic tests. The aim of this study was to determine these costs. Methods A total of 203 haematology patients were enrolled into the study and followed for a median of 556 days. Data were prospectively collected on antifungal drugs, diagnostic tests, length of stay and antibiotic usage. Results The overall mean (IQR) cost of care per patient (using UK-based reference costs) was £88 911 (45 339–121 594), £61 509 (39 748–78 383), £50 332 (23 037–72 057) and £34 075 (19 928–43 900) for proven/probable IFD, possible IFD, not classified and no evidence of IFD, respectively (P < 0.001). The attributable cost of IFD was £54 836. Inpatient hospital stay accounted for nearly 74% of costs. In proven/probable IFD inpatient care, antifungals, antibiotics and IFD status accounted for 68%, 25%, 5% and 2%, respectively, compared with 85%, 11%, 2% and 2%, respectively, for no IFD (P < 0.001). Among the allogeneic transplant patients, £36 914 (60%) of the total cost (£60 917) was used during the first 100 days. Conclusions IFD was associated with longer length of stay and higher total overall cost of care, with attributable costs greater than £50 000 per case of IFD. Costs for inpatient stay far outstrip the cost of antifungal agents.