The aim of this study was to report a unique case of microsporidial keratitis over deep anterior lamellar keratoplasty after transepithelial photorefractive keratectomy surgery that was successfully treated with therapeutic lamellar keratoplasty without recurrence at King Khaled Eye Specialist Hospital in Riyadh, Saudi Arabia. The patient presented with recurrent attacks of eye pain, redness, photophobia, and decreased vision. The patient was initially treated as a case of presumed herpetic keratouveitis using antiviral medication and topical steroids with partial improvement. During the last episode, the condition deteriorated and patient underwent therapeutic lamellar keratoplasty. Histopathology indicated an infected graft with evidence of microsporidial infection. The patient was discharged with complete corneal epithelial healing and no signs of recurrence during follow-up. Microsporidial infection is a rare cause of stromal keratitis that affects both immunocompetent and immunosuppressed patients. Microsporidia should be suspected after surface ablation refractive surgery if the patient presents with recurrent symptoms of keratoconjunctivitis or stromal keratitis that are partially responsive to topical steroid therapy.