The aim of this study was to describe the indications and outcomes of flap amputation after laser in situ keratomileusis (LASIK) at a referral-based institution. In this retrospective consecutive case series, medical records of patients who underwent LASIK flap amputation at Mayo Clinic, Rochester, MN, between January 1, 1998, and January 31, 2023, were reviewed. Fifteen eyes (15 patients) underwent flap amputation during the study period. The median age was 45 years (range, 25-71 years), and 8 patients (53%) were men. The median uncorrected visual acuity before flap amputation was 20/200 (range 20/40-hand motions). Indications for flap amputation included epithelial ingrowth (n = 6, 40%), infectious keratitis (n = 6, 40%), diffuse lamellar keratitis (n = 1, 7%), vegetative foreign body (n = 1, 7%), and astigmatism from fixed flap striae (n = 1, 7%). The median duration of follow-up was 8 months (range 1-234 months). Subsequent corneal interventions included chelation of calcific band keratopathy (n = 1, 7%), lamellar keratoplasty (n = 1, 7%), penetrating keratoplasty (n = 2, 18%), keratoprosthesis (n = 1, 7%), and rigid contact lens wear (n = 4, 27%). The final median best visual acuity was 20/25 (range 20/20-20/200). Compared with noninfectious indications for flap amputation, eyes with infectious indications had worse baseline median uncorrected visual acuity (hand motions vs. 20/63, P < 0.001), were more likely to undergo major corneal surgical intervention (50% vs. 11%), and had worse final median best visual acuity (20/50 vs. 20/20, P = 0.018). LASIK flap amputation is sometimes necessary to control threatening corneal diseases. Excellent visual outcomes were achieved in most cases, albeit with additional intervention or rigid contact lens wear.