Background: This observational study was conducted to document the efficacy and safety of the use of micafungin (Mycamine) as an empirical antifungal agent in febrile neutropenic patients. Methods: Micafungin was administered for sustained fever (>38.4°C) on days 3–5 following the initiation of empirical antibiotic therapy. The overall success rate and side effects were evaluated. Results: A total of 47 patients with acute myeloid leukemia, acute lymphoblastic leukemia, myelodysplastic syndrome and lymphoma were enrolled in the study. The overall success rate of micafungin was 61.7% (29/47). A total of 3 patients (6.4%) experienced grade 3/4 elevations in their aspartate aminotransferase levels, and 10 patients (21%) experienced grade 3/4 hyperbilirubinemia, 9 of which resolved. Four patients died of septic shock. Younger patients (<50 years) and patients with acute lymphoblastic leukemia exhibited a better response to micafungin than other patients. Patients that were less profoundly neutropenic (≧0.05 × 109/l) also had a better response to micafungin, as did the patients who recovered from their fever or neutropenia. Conclusion: Micafungin has an excellent efficacy (61.7%) and safety profile when used as an empirical antifungal agent in febrile neutropenic patients with hematological disorders.