The literature is lacking data concerning the prognosis in cats suffering from naturally occurring acute onset of thoracolumbar (TL) spinal cord injury that are undergoing rehabilitation therapy. Therefore, we investigated the effect of physical rehabilitation in cats suffering from naturally occurring TL spinal cord injury. The medical records of 36 cats with acute onset of TL spinal cord injury that were selected for rehabilitation treatment were reviewed. Twenty-nine cats underwent an intensive physical rehabilitation protocol in the clinic (group 1), whereas the owners of seven cats declined physical rehabilitation (group 2). In group 1, seven cats had pelvic limb deep pain perception (DPP), which was significantly associated with the functional recovery of voluntary ambulatory status (p = 0.010) and voluntary micturition (p < 0.001). Spinal walking was achieved in 10/22 (45%) of the cats without DPP, and none regained voluntary micturition. In group 2, no cats regained ambulatory status or voluntary micturition, although pelvic limb DPP was present in three patients. Treatment with a clinic-based rehabilitation program and the presence of a crossed extensor reflex were significantly associated with a higher possibility of regaining functional ambulatory status (p < 0.010), but there was no difference in the recovery of voluntary micturition between the groups. Thus, cats with severe, naturally occurring, acute onset of TL spinal cord injury may benefit from physical rehabilitation. In the case of the loss of DPP, the acquisition of spinal walking is possible, despite the high possibility of a persistent neurologically dysfunctional bladder.