Purpose: To report the successful use of intravitreal (IVT) caspofungin in the management of drug-resistant bilateral endogenous fungal endophthalmitis and to assess its clinical safety and efficacy. Methods: A single case was reviewed. Results: A 40-year-old woman developed bilateral endogenous endophthalmitis following ureteric stent removal. The right eye, which presented with pain, redness, and significant vision loss, was successfully treated with pars plana vitrectomy and IVT voriconazole. The left eye, initially managed with voriconazole and amphotericin B, deteriorated despite repeated antifungal injections, necessitating vitrectomy. Vitreous cultures grew Candida albicans resistant to fluconazole and voriconazole but sensitive to amphotericin B and caspofungin. IVT caspofungin (50 μg/0.1 mL) was administered in the left eye for persistent infection, leading to significant clinical improvement without drug-related adverse effects. At the final follow-up, infection was controlled in both eyes, and the patient’s best-corrected visual acuity was 20/32 (0.2 logMAR) OD and 20/40 (0.3 logMAR) OS. Conclusions: IVT caspofungin appears to be a safe and effective treatment option for fungal endophthalmitis resistant to conventional antifungal agents and may serve as a valuable adjunct in refractory cases.