Purpose: To report an unusual case of deep keratomycosis after Ahmed glaucoma valve (AGV) implantation. Methods: A 70-year-old male presented with a deep corneal stromal infiltrate, without epithelial involvement, 3 weeks after a successful AGV implantation for neovascular glaucoma. Microscopic examination of the anterior chamber exudates revealed fungal filaments on smear, and white fungal colonies were observed on the Blood agar and Sabouraud dextrose agar. The fungus was identified as Aspergillus flavus. Results: The patient was treated with oral and topical 1% voriconazole. Ten weeks after the treatment, the corneal infiltrate resolved, resulting in a vascularized scar. Conclusion: As recalcitrant keratomycosis of the deep corneal layers may occur after AGV implantation, early identification and prompt treatment may help to achieve complete resolution of the infection and salvage the eye.