We describe a case of Candida parapsilosis endophthalmitis with a consecutive keratitis after phacoemulsification and posterior chamber intraocular lens implantation in an otherwise healthy eye. Despite aggressive medical and surgical management during a 2-year period, multiple episodes recurred, with the development of an intracapsular plaque and an infectious nidus on the corneal endothelium 6 months after the initial presentation. After subtotal removal of the culture-positive capsule, intravitreal and topical amphotericin B, and oral fluconazole, the inflammation improved. However, the corneal endothelial plaque persisted with recurrent inflammation 2 months later, prompting debridement of the culture-positive plaque and further removal of the culture-negative capsular remnants and lens implant. The infection was quiescent for the subsequent 12-month period until recurrent intraocular inflammation developed with enlargement of the endothelial plaque. Culture of this plaque was again positive for C. parapsilosis. After debridement and intraocular and topical amphotericin B, the eye has now been quiescent for 13 months. This case demonstrates the development of a secondary keratitis in an eye affected by pseudophakic C. parapsilosis endophthalmitis, with the posterior cornea serving as a sanctuary site for the fungus despite aggressive management leading to recurrent infection 1 year after the clinical disease appeared to be quiescent.