Introduction: The cornea may become infected and perforated after epithelium-on collagen crosslinking. Case presentation: A healthy 33-year-old male who underwent corneal collagen crosslinking in both eyes developed a purulent keratitis and bilateral corneal perforations, requiring bilateral penetrating keratoplasties. He was exposed to methicillin resistant staphylococcus aureus (MRSA) by a family member with a tracheostomy and was treated with MRSA-directed antibiotics. After prolonged recovery and treatment of his infection, he had acceptable but limited uncorrected visual acuity, with excellent corrected visual acuity. Conclusion: While epithelium-on crosslinking is commonly thought to be associated with a lower risk of postoperative infection, this case illustrates that even epithelium-on treatment may present the patient with a risk of infection. Patients in higher risk groups who are exposed to infectious disease may be more predisposed.