Fluconazole was reported to be an effective alternative to Amphotericin B for candidal endophthalmitis. However, the dose for systemic use had not been determined and few pathological reports on its use have been published. An epiretinal membrane harvested from a regressed candidal endophthalmitis in a patient treated with fluconazole (200 mg/day) was sent for pathologic study. On the inner side of the retina, a granuloma was found. Fungal debris was found within the center of the granuloma, but an intact fungus was seen next to the granuloma. Pathologic study showed incomplete treatment in this case, although systemic status had improved. The use of systemic fluconazole should be maintained for a longer period of time to treat candidal endophthalmitis.