To report a method of treatment for through-the-flap multibacterial ulcerative keratitis after laser in situ keratomileusis (LASIK). Bacterial ulcerative keratitis after LASIK was treated with topical and systemic antibiotics followed by flap lifting, cleaning, and phototherapeutic keratectomy (PTK). Follow-up examinations included in vivo confocal microscopy, corneal topography, and wavefront analysis. Rapid recovery of the ulcerative keratitis was observed after flap lifting and cleaning of the interface and PTK combined with topical and systemic antibiotics. Two years postoperatively, corneal topography showed a slight depression of the ulcer area and decentration of the photoablation. Wavefront analysis revealed an irregular scan with a pronounced coma-like aberration, which with a wavefront-guided custom test lens correction provided 20/16 visual acuity. Ulcerative bacterial keratitis is a possible sight-threatening complication of LASIK refractive surgery. Lifting and rinsing the flap combined with cleaning of the flap interface with PTK may be helpful in these conditions when regression of the ulcer does not occur with topical and oral antibiotic treatment.