This study assessed the safety and efficacy of transepithelial crosslinking (CXL) using femtosecond (FS) laser-machined epithelial microchannels (MCs) followed by UVA CXL compared to FS laser (NLO CXL) in rabbits. The epithelium of 36 rabbits was machined to create 2- by 25-µm MCs at 400 MCs/mm2. Eyes were treated with 1% riboflavin (Rf) solution for 30 minutes, rinsed, and then crosslinked using UVA or NLO CXL. Rabbits were monitored by epithelial staining, optical coherence tomography (OCT) imaging, and esthesiometry. After sacrifice at 2, 4, or 8 weeks, corneas were examined for collagen autofluorescence and immunohistochemistry. NLO CXL showed no epithelial damage compared to UVA CXL, which produced on average 23.89 ± 5.6 mm2 epithelial defects that healed by day 3. UVA CXL also produced loss of corneal sensitivity averaging 0.83 ± 0.24 cm force to elicit a blink response that persisted for 28 days and remained significantly lower than control or NLO CXL. OCT imaging detected the presence of a demarcation line only following UVA CXL but not NLO CXL. Even with improved transepithelial Rf penetration, UVA CXL resulted in severe epithelial damage, loss of corneal sensitivity, and delayed wound healing persisting for a month. When MCs were paired with NLO CXL, however, these issues were mostly negated. This suggests that MC NLO CXL can achieve a faster visual recovery without postoperative pain or risk of infection. UVA CXL is a successful procedure, but there is a need for a transepithelial protocol. The combination of MCs and NLO CXL is able to keep the benefits of UVA CXL without causing epithelial damage.