Purpose: The purpose of this study was to evaluate the efficacy of temporary conjunctival flap with topical natamycin and oral voriconazole compared with medical treatment only in reducing the rate of perforation in high-risk fungal keratitis. Methods: Sixty-two eyes of 62 patients with severe fungal keratitis were examined; only 54 patients were enrolled and divided randomly into 2 groups. The first group received medical treatment only in the form of topical natamycin 5% together with oral voriconazole 200 mg, while the second group received the same medical treatment plus a temporary conjunctival flap that was removed after 2 weeks. Five patients were lost during the follow-up, and only 49 patients were statistically analyzed. All patients were examined frequently until reepithelialization or the development of perforation. Results: Fifteen perforations were reported, with a higher rate among the medical group (48%) compared with the conjunctival flap group (12.5%), with P value ,0.05. A significant delay was noted in reepithelialization time in the medical group compared with the conjunctival flap group (mean time was 21.69 ± 6 5.41 and 15.36 ± 6 2.2 days, respectively), with P value = 0.001. Significant improvement in visual acuity was reported over time when comparing baseline versus 3-month visual acuity in the same group using paired t sample test (P value was 0.003 and ,0.001 in the first and second group, respectively). Conclusions: Temporary conjunctival flap is associated with a lower perforation rate compared with medical treatment only in severe fungal keratitis, which can provide a cheap and available alternative to therapeutic penetrating keratoplasty.