Background: The aim of this study was to analyze the long-term topographic and refractive outcomes of corneal cross-linking (CXL) in keratoconus. Methods: We used a retrospective observational study of patients with keratoconus who underwent CXL with a minimum follow-up of 5 years. Patients’ refractive and topography data (corrected distance visual acuity, sphere, cylinder, average and maximum keratometry, and corneal aberrations) were collected. Results: A total of 112 patients/150 eyes (mean age: 33.2 ± 10.7 years; range: 13–61) were included. The mean follow-up was 5.87 ± 1.35 years (range: 5–10). At the last follow-up visit, an improvement in CDVA, spherical and cylindrical refraction, average and steepest keratometry, and corneal aberrations were observed (p < 0.05), with the exception of trefoil. At the last visit, 49 (34.8%) and 31 (22.0%) eyes had an improvement beyond 1D in their spherical and cylindrical power, respectively, and 43 (28.7%) eyes had a flattening of their steepest keratometry. Progressive improvement over time was observed for spherical refraction; max and mean-K; as well as corneal RMS, total, high, coma, and spherical aberrations (p < 0.05). More severe disease at the baseline correlated with an improvement in corneal aberrations over time. Conclusions: In addition to a progressive improvement in refractive and keratometric indices, corneal aberrations also demonstrate a steady decline with long-term follow-up after CXL, which was more pronounced in more severe patients.