Fungal endophthalmitis is a rare condition often associated with poor prognosis. We present a case of postoperative acute fungal endophthalmitis caused by the yeast-like fungus Stephanoascus ciferrii (Candida ciferrii). The fungus was resistant to fluconazole, voriconazole, and amphotericin B but susceptible to caspofungin. Because the degree of vitreal penetration of caspofungin after its intravenous administration is unclear, we performed multiple intravitreal injections, first with 50 µg/0.1 ml and then with 250 µg/0.1 ml caspofungin. Despite the recurrence of symptoms, intravitreal injection of caspofungin finally abolished the inflammation and achieved ambulatory vision that persisted until 1 year of follow-up. To our knowledge, this is the first report of S. ciferrii endophthalmitis and its successful treatment with intravitreal caspofungin.