Abstract Background Corneal ectasia after small-incision lenticule extraction (SMILE) is uncommon. To our knowledge, this is the first report of 3-year results of combined phototherapeutic keratectomy (PTK) and corneal collagen cross-linking (CXL) for corneal ectasia after SMILE. Case presentation Herein, we describe a case of prominent corneal ectasia after SMILE treated with PTK combined with CXL 3 years ago. After surgery, maximum corneal keratometry, mean corneal keratometry, spherical equivalent and uncorrected distance visual acuity were significantly improved at follow-up intervals. Conclusions Transepithelial PTK combined with CXL for corneal ectasia after SMILE may be an effective and safe treatment in the long term.