The prognosis of fungal endophthalmitis is usually poor. Currently, it is confusing in the drugs and surgical treatment and has been explored and progressed. Traditional drugs include amphotericin B, fluconazole and flucytosine. A new generation of drugs includes liposomal amphotericin B, Voriconazole, and caspofungin. Vitrectomy combined with systemic, topical and intraocular application of drugs is particularly important for the treatment of fungal endophthalmitis. This article reviews the current and ongoing development of drugs and surgical treatment of fungal endophthalmitis.