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Sterile infiltrates following collagen crosslinking (CXL) are an uncommon complication, typically reported in the early postoperative period. A patient in her mid-20s was diagnosed with keratoconus and underwent an uneventful CXL procedure. She demonstrated normal healing of the corneal epithelial defect postoperatively, and bandage contact lens was removed on postoperative day 4. The patient presented with peripheral corneal infiltrates on day 15 following surgery. The infiltrates were noted 1–2 mm from the limbus at the 8–10 o’clock position. Lid examination revealed mild Meibomian Gland Dysfunction (MGD) in both eyes. Autoimmune work up was unremarkable. A diagnosis of late-onset sterile keratitis was made, and topical steroids were intensified under antibiotic cover. The infiltrates resolved gradually over 3 weeks, leaving a residual scar. CXL may result in prolonged immune alterations in the cornea, rendering it more sensitive to antigenic stimuli.