To report a patient who presented with epithelial ingrowth caused by viral keratoconjunctivitis 3 months after LASIK surgery. A 41-year-old man presented with decreased visual acuity in the right eye, which had developed about 3 weeks before. He had undergone LASIK surgery 3 months prior without complications. Two months after the surgery, he was treated for viral conjunctivitis. During the treatment period, filamentary keratitis developed, and a therapeutic bandage contact lens was applied for 2 weeks. Upon presentation, examination revealed a corrected visual acuity of 20/100 and irregular epithelial sheets under the edematous flap. The flap was lifted, and the in-grown epithelium was removed. The flap was repositioned with double continuous 10 - 0 nylon sutures. Post-operatively, the patient developed a mild diffuse lamellar keratitis that resolved rapidly with topical corticosteroid treatment. At 2 months, the corrected visual acuity was 20/20 without interface opacities. As the patient showed no complications prior to viral conjunctivitis, we suspect that the viral infection caused edema of the corneal flap, which caused epithelial ingrowth under the flap. Patients who have viral conjunctivitis after LASIK surgery should be examined carefully and managed with consideration of flap complications.