OBJECTIVE To compare and evaluate the efficacy of topical 0.1% micafungin (MCFG) and topical 0.2% fluconazole (FCZ) in the treatment of Candida fungal keratitis. METHODS Twenty-nine eyes of 29 patients who were diagnosed as having Candida fungal keratitis, proven by corneal culture isolates, were investigated in this prospective study. Patients were divided into a MCFG treatment group (12 eyes) and an FCZ treatment group (17 eyes). Age, gender, initial status of ulcer (ulcer size and degree of injection), initial and final best-corrected visual acuity (BCVA), healing periods, final status of cornea and recurrences in each group were studied and compared. RESULTS There were no significant differences in relation to age, gender, ulcer size and degree of injection before treatment between the two groups. There were also no significant differences in the healing periods until complete epithelialisation (MCFG treatment group (41.3 ± 38.0 days); FCZ treatment group (34.4 ± 37.7 days)), change in BCVA, corneal clarity/opacification, perforation and recurrence status at the final examination between the two groups. CONCLUSIONS The efficacy of 0.1% MCFG eye-drops appears to be comparable with that of 0.2% FCZ eye-drops in the treatment of Candida fungal keratitis.