Purpose: To report the intraoperative corneal pachymetry changes during accelerated corneal cross-linking (A-CXL) in progressive keratoconus patients with thin corneas. Methods: Thirty-six eyes (mean age, 22.26 ± 4.02 years) with progressive keratoconic thin corneas (<400 μm without epithelium) who underwent A-CXL with ultraviolet (UV)-A (UVA) (9 mW/cm2) using isotonic riboflavin5-phosphate 0.1% with 1.1% hydroxypropyl methycellulose (RF-HPMC, MedioCROSS M) were included in this retrospective study. Intraoperative corneal pachymetric changes were noted before the procedure, after removal of epithelium, after RF-HPMC instillation, before and after UV irradiation. The mean of corneal pachymetric values were compared statistically. Results: The mean corneal pachymetry reduced from 415.72 ± 29.66 to 369.50 ± 23.45 μm after removal of the epithelium (p < 0.05). After the application of RF-HPMC solution the mean thinnest corneal pachymetry (TCP) increased to 412.89 ± 26.94 μm. Statistically significant increase was observed in TCP after saturation with RF-HPMC (p = 0.001). The mean corneal pachymetry before and after UVA irradiation was 419.86 ± 10.41 and 417.47 ± 8.25 μm, respectively (p > 0.05). Conclusions Isotonic RF-HPMC lead to a significant increase in intraoperative mean TCP. RF-HPMC seems to be a favorable riboflavin option in keratoconus patients with thin corneas.