The objective of this study was to investigate the effects of autologous neurogenically induced bone marrow-derived mesenchymal stem cells (NIBM-MSCs) in two dogs suspected to have fibrocartilaginous embolic myelopathy (FCEM). Both dogs were paraplegic without deep pain perception (DPP) and tentatively diagnosed by MRI. Autologous NIBM-MSCs (5 × 106) were transplanted into the lumbar subarachnoid space two times with a 21-day interval for each patient. Based on a 21-month follow-up of the treated animals, the transplantation of NIBM-MSCs seems to be promising in subjects with FCEM lacking DPP.