OBJECTIVES: To determine the cost-effectiveness of using anidulafungin and fluconazole for the treatment of invasive candidiasis from the Malaysian government hospital’s perspective. METHODS: A decision analytic model was employed to depict the economic consequences of using anidulafungin or fluconazole in the Malaysian government hospitals. Transition probabilities (i.e. treatment success or treatment failure) were obtained from a randomised controlled trial. For data that was not available in the published literatures, model assumptions were made. Sensitivity analyses (i.e. one-way sensitivity, threshold, scenario and probabilistic sensitivity analyses) were conducted to assess the robustness of the model outcome. RESULTS: Treatment with anidulafungin (RM20,412) was associated with an incremental cost of RM8,015 when compared to fluconazole (RM12,397). Anidulafungin was estimated to provide an additional 0.74 life-years (LYs) saved compared to fluconazole. Therefore, treatment with anidulafungin was associated with an ICER of RM10,831 per LYs saved. Drug acquisition was the main cost driver for anidulafungin while hospitalisation cost was the major cost driver for the fluconazole arm. The model outcome was most sensitive to the changes in probability of patients with treatment success in the anidulafungin arm and drug acquisition cost of anidulafungin. CONCLUSIONS: Anidulafungin appears to be a cost-effective therapy compared to fluconazole in treating invasive candidiasis from the Malaysian government hospital’s perspective.