To present a case of a late, deep stromal scar in a 22-year-old patient with forme fruste keratoconus who underwent combined corneal cross-linking and photorefractive keratectomy (PRK). Topography-guided corneal cross-linking combined with corneal PRK (without complications) was performed in both eyes with a delay of 2 weeks between each eye. At the 5-month postoperative examination of the right eye, a localized corneal haze was circumscribed to the posterior deep stroma, signifying a decrease of visual acuity. However, this improved partially and temporarily when treated with topical corticoids during 2 years of follow-up and then reoccurred, affecting the corrected distance visual acuity. To the authors' knowledge, this is the first documented, clinical case presenting a deep stromal affectation without endothelial decompensation and visual acuity affectation as a postoperative complication following topography-guided PRK and corneal cross-linking.