PurposeTo employ ultrahigh‐resolution (UHR) optical coherence tomography (OCT) for investigation of the early wound healing process in corneal epithelium.MethodsA custom‐built UHR‐OCT system assessed epithelial healing in human keratoconic cornea after epi‐off crosslinking (CXL) procedure and a wound healing model in rabbits with iatrogenic corneal injury. 3D OCT data sets enhanced obtaining epithelial thickness maps and evaluation of reepithelization stage. Accompanying changes in deeper corneal microarchitecture were analysed.ResultsThe mean central corneal thickness in 40 eyes with keratoconus at baseline was 482.7 ± 38.2 μm, while mean central epithelial thickness (CET) was 43.8 ± 6.4 μm. At the final visit 20 ± 5 days post‐CXL procedure, CET was 35.0 ± 5.8 μm, significantly thinner after reepithelization (p < 0.001). Surgical success was assessed at the final visit through the demarcation line (DL), identified at 43.7 ± 13.5% stromal depth. In rabbits, the mean CET in 20 eyes at baseline was 35.9 ± 2.6 μm. In rabbits that revealed complete wound closure (10/20 eyes) at the last study day at 72 hr, CET was significantly thinner compared to baseline (30.4 ± 2.8 μm versus 35.4 ± 2.9 μm, p = 0.005). An intra‐stromal landmark indicating early keratocyte apoptosis was measured at 30.0 ± 5.1% stromal depth. Epithelial thickness maps showed the time–course of corneal healing.ConclusionUltrahigh‐resolution (UHR)‐OCT provided precise assessment of epithelial wound and its healing by 3D‐mapping. In addition, microarchitectural changes in the cornea in early phases of epithelial healing were revealed.