Mooren's ulcer is an idiopathic peripheral ulcerative keratitis whose pathogenesis is thought to be due to an autoimmune reaction. The first-line treatment for Mooren's ulcer is the use of topical steroids, which can be difficult to discontinue. The 76-year-old patient in this case was receiving topical steroids for bilateral Mooren's ulcer and developed a feathery corneal infiltration and perforation in the left eye. On suspicion of a fungal keratitis complication, we started topical voriconazole treatment and performed lamellar keratoplasty. Topical betamethasone was continued twice a day. The identified causative fungus was Alternaria alternata, which is known to be susceptible to voriconazole. The minimum inhibitory concentration of voriconazole was later proven to be 0.5 μg/mL. After 3 months of treatment, the residual feathery infiltration disappeared and the left vision recovered to 0.7. In this case, topical voriconazole was effective, and the eye was successfully treated with continuing topical steroids. Fungal species identification and antifungal susceptibility test proved helpful for symptom management.