Regenerative medicine using stem cells from various sources are emerging treatment modality in several refractory diseases in veterinary medicine. It is well-known that stem cells can differentiate into specific cell types, self-renew, and regenerate. In addition, the unique immunomodulatory effects of stem cells have made stem cell transplantation a promising option for treating a wide range of disease and injuries. Recently, the medical demands for companion animals have been rapidly increasing, and certain disease conditions require alternative treatment options. In this review, we focused on stem cell application research in companion animals including experimental models, case reports and clinical trials in dogs and cats. The clinical studies and therapeutic protocols were categorized, evaluated and summarized according to the organ systems involved. The results indicate that evidence for the effectiveness of cell-based treatment in specific diseases or organ systems is not yet conclusive. Nonetheless, stem cell therapy may be a realistic treatment option in the near future, therefore, considerable efforts are needed to find optimized cell sources, cell numbers and delivery methods in order to standardize treatment methods and evaluation processes.