Purpose: To report a case of delayed onset infectious crystalline keratopathy after corneal cross-linking (CXL). Methods: Slit-lamp examination, confocal microscopy, anterior segment optical coherence tomography imaging, and corneal culture were performed to characterize the corneal opacification. Results: A 49-year-old man presented with progressively worsening vision in the left eye 8 months after uncomplicated epithelium-off CXL for keratoconus. Examination demonstrated focal central corneal stromal thinning with surrounding stromal opacification. Confocal microscopy did not demonstrate evidence of parasitic or fungal infection. Two months later, gray-white crystalline stromal opacities were observed surrounding the area of central stromal thinning, consistent with infectious crystalline keratopathy. Corneal scrapings of the left eye were obtained, which were positive for Enterococcus faecalis. After cessation of topical loteprednol and initiation of topical vancomycin and linezolid, the stromal infiltrate increased in size and a hypopyon developed but had resolved before the discontinuation of 7 weeks of topical antibiotic therapy. A deep anterior lamellar keratoplasty was performed 6 weeks later, with no recurrence of infection 10 months after surgery. Conclusions: Infectious crystalline keratopathy can present more than 6 months after CXL. Progressive corneal stromal thinning associated with stromal opacification should raise suspicion of this rare late onset complication of CXL and prompt corneal scraping for stains and cultures to rule out an indolent infectious process.