A 23-year-old woman was referred for management of intractable post-laser in situ keratomileusis (LASIK) keratitis due to atypical mycobacteria in the left eye. Corrected distance visual acuity was 20/20 in the right eye and counting fingers at 3 meters in the left eye. Slitlamp examination revealed multiple infiltrates in the flap interface and severe corneal stromal melting with thinning. Despite maximum antibiotic therapy for 7 days, the keratitis continued to worsen. A penetrating keratoplasty (PKP) was scheduled. While waiting for a corneal graft, corneal collagen crosslinking (CXL) with riboflavin and ultraviolet-A was proposed as an alternative treatment. Flap amputation and limited phototherapeutic keratotomy (PTK) (10 μm) were also performed. One week postoperatively, all infiltrates and stromal edema had resolved. At 3 months, the uncorrected distance visual acuity improved to 20/35. Corneal crosslinking after flap amputation and limited PTK was an effective treatment for severe intractable post-LASIK keratitis with corneal melting and obviated PKP.