Candida auris is an emerging multidrug-resistant fungus usually associated with hospital-acquired infections leading to bloodstream infections and panophthalmitis. We report a rare case of late-onset postoperative fungal endophthalmitis caused by Candida auris. The patient showed poor response to intravitreal voriconazole injection, and his clinical condition worsened. Intravitreal injection of caspofungin was given based on the opinion of an infectious disease specialist along with the culture sensitivity report. Prompt identification and appropriate management led to an excellent outcome. Caspofungin could be a safe intravitreal alternative in cases with resistant candida endophthalmitis.