The regenerative capacity of corneal endothelial cells (CECs) differs between species; in bigger mammals, CECs are arrested in a non-proliferative state. Damage to these cells can compromise their function causing corneal opacity. Corneal transplantation is the current treatment for the recovery of clear eyesight, but the donor tissue demand is higher than the availability and there is a need to develop novel treatments. Interestingly, rabbit CECs retain a high proliferative profile and can repopulate the endothelium. There is lack of fundamental knowledge to explain these differences. Gaining information on their transcriptomic variances could allow to identify CEC proliferation drivers. In this study, we analyzed human, sheep, and rabbit CECs at the transcriptomic level. To understand the differences across each species, we generated a pipeline for the analysis of pathways with different activity. Our results revealed that 52 pathways had different activity when comparing species with non-proliferative CECs (human and sheep) to species with proliferative CECs (rabbit). Our results showed that Notch and TGF-β pathways had increased activity in species with non-proliferative CECs, which might be associated with their low proliferation. Overall, this study illustrates transcriptomic pathway-level differences that can provide leads to develop novel therapies to regenerate the corneal endothelium.