Aim: To compare outcomes of transepithelial collagen crosslinking (TECXL) and contact lens-assisted collagen crosslinking (CACXL) for progressive keratoconus with borderline corneal thickness. Materials and methods: In this prospective, comparative, interventional series, twenty eyes with progressive keratoconus and a preoperative ‘epithelium on’ minimal corneal thickness (MCT) of 350-420 μm, were randomized to undergo TECXL (n = 11 eyes) or CACXL (n = 9 eyes) using hydroxypropyl methylcellulose (HPMC) based 0.25% and 0.1% riboflavin respectively. Primary outcomes evaluated were demarcation line depth on anterior segment optical coherence tomography (ASOCT) 1 month postoperatively: change in maximum keratometry (Kmax) and endothelial cell density (ECD) at 6 months from baseline. Postoperative pain in the first 4 days and haze at 6 months were also compared between the two techniques. Results: Preoperative ‘epithelium on’ MCT in the TECXL (394.3 ± 12.6 μm)and CACXL (385.6 ± 13.8 μm) groups was comparable (p = 0.15); mean demarcation line depth was 74.6% (294.4 ± 57.1 μm) and 80% (308.2 ± 84.2 μm) respectively (p = 0.66). Regression (reduction of Kmax by >1 diopter) or stabilization (change in Kmax of < ± 1D) was seen in 91% (n = 10) and 89% (n = 8) eyes of the TECXL and CACXL groups, respectively. ECD at baseline and last follow up was comparable in each group (p >0.05). Postoperative pain in the first four days and haze at 6 months post the CXL procedure were also comparable (all p's >0.05). Conclusion: Using HPMC riboflavin, both TECXL and CACXL had good clinical efficacy and equivalent patient comfort without compromising endothelial safety, in keratoconus patients with thin corneas. Clinical significance: TECXL and CACXL are simple, costeffective techniques to arrest progression in keratoconus patients with borderline corneal thickness and may decrease the need for future surgical interventions like lamellar or penetrating keratoplasty.