Purpose Comparative prospective mid-term 24 months functional analysis after Epi-off and Epi-on Riboflavin UV A corneal cross-linking (CXL) in patients affected by progressive keratoconus (KC). Methods Functional analysis comprised 30 eyes of 24 patients (15 - 26 years) treated by epi-on trans-epithelial CXL procedure and 30 eyes of 24 patients (10 - 26 years) treated by standard epi-off CXL. Therapy was performed according to the Siena protocol by using the Vega CBM (Caporossi-Baiocchi-Mazzotta) X linker (CSO, Florence, Italy) at Siena University. Results At 24 months follow-up patients showed a mean gain in UCVA of +0.2, +Snellen lines in the epi-off group while in the epi-on group after a mean improvement of 1 Snellen Line at 3 months, uncorrected visual acuity gradually returned to baseline. BSCVA gained by a mean of +0.2 Snellen lines in the epi-off procedure while in the epi-on patients no significant improvement was recorded at 24 moths follow-up. Kmax was reduced by a mean value of −0.6D, and Coma values improved by a mean of −0.45 μm in the epi-off group. No significant variation in K readings and coma values were recorded in the epi-on treatment. Conclusion Epi-off CXL showed a constant improvement of functional data while the epi-on procedure showed a relative instability with a regression of functional outcomes returning to baseline at 24 months of follow-up. In patients with progressive keratoconus under 26 years with corneal thickness over 400 microns epi-off cross-linking should be the first choice therapy. According to actual limitations epi-on procedure should be reserved in patients over 26 years with low KC progression or in patients with thinnest point under 400 microns.