Photorefractive keratectomy (PRK) was performed to treat corneal epithelial basement membrane dystrophy (EBMD) found after femtosecond laser-assisted laser in situ keratomileusis (FS-LASIK) in a 29-year-old man with previous silent cornea. The patient was diagnosed with post-FS-LASIK EBMD by slitlamp examination and in vivo confocal microscopy (IVCM). Initial treatment with topical lubricants and alcohol soaking was unsuccessful, and the patient continued to have blurred vision and discomfort. The patient underwent a PRK procedure, and the symptoms resolved dramatically; residual refractive errors were also corrected. IVCM revealed a characteristic presentation of EBMD before PRK and normal corneal epithelium after treatment. Patients with asymptomatic EBMD might suffer from recurrent corneal erosions after FS-LASIK. Surface ablation including PRK might lead to successful treatment outcomes, and IVCM might provide helpful information before and after treatment.