Purpose: This study aimed to present two patients with delayed-onset, endogenous fungal keratitis after treatment for fungal endophthalmitis after cataract surgery., Methods: The authors retrospectively reviewed the clinical course of two patients in whom deep stromal fungal keratitis developed 2 weeks and 3 months, respectively, after apparent successful aggressive therapy for fungal endophthalmitis. Before the onset of the keratitis, both patients underwent vitrectomies with intraocular injection of 7.5 to 10.0 mcg amphotericin B, as well as treatment with systemic fluconazole and topical antifungal therapy. In case 1, a pre-existing prosthetic intraocular lens and lens capsular bag were removed at the time of vitrectomy, whereas in case 2, the intraocular lens was left in place and a posterior capsulectomy was performed., Results: The keratitis worsened in both patients, despite intensive systemic and topical antifungal therapy. Both patients underwent therapeutic penetrating keratoplasties. In case 1, this resulted in successful resolution of the infection and no recurrences 3 months after the transplant. The corneal transplant was complicated by an expulsive choroidal hemorrhage in the other patient. Fusarium solani was cultured from the initial vitrectomy specimen in patient 1, and although it was not cultured from the keratitis, septate hyphal elements were present on histopathologic examination. The causative organism in case 2 was Acremonium kiliense, which was cultured from both the original vitrectomy specimen and the deep corneal stromal infiltrate., Conclusions: Fungal organisms may not be eradicated completely from eyes with endophthalmitis despite aggressive therapy and apparent initial successful treatment. These patients need to be monitored for prolonged periods, and treatment should be reinitiated at the earliest sign of recrudescence of infection.