Background Acute spinal cord injury (ASCI) can lead to paraplegia or quadriplegia, the treatment of which has been a major problem. New therapeutic approaches in developing carbon nanotubes (CNT) functionalized with the Nafion nanocomposite, a sulfonated tetrafluoroethylene copolymer, have been shown to increase the length of selected neurites in vitro. Objective We hypothesized that the administration of the CNT/Nafion nanocomposite after experimental SCI will promote regeneration of axons into the lesion cavity and the functional recovery of the hind limbs in a rat model. Methods To evaluate this hypothesis through this experimental research paper, transection SCI was induced at the T9-T10 vertebral level in adult female rats. One week after transection, the epicenter of the lesion was injected with 25 lL of vehicle (saline), or 1 lg/mL, 10 lg/mL, or 100 lg/mL of CNT/Nafion nanocomposite. Behavioral analysis was carried out by assessing tail flick, chronic pain or mechanical allodynia, motor coordination, and the results of the rotarod test performed pre- and post-surgery, on days 3, 7, 14, 21 and 28, using the tail flick analysis, Noldus CatWalk gait analysis, open-field locomotor test, and Rotarod test. At 28 days post-injection, the rats were euthanized and spinal cord tissue was extracted. Results We found that post-SCI, administration of the CNT/Nafion nanocomposite resulted in decreased lesion volume, increased neurofilament-positive fibers and corticospinal tract fibers in the lesion, and no increase in reactive gliosis (P < 0.001). Additionally, post-SCI administration of CNT/Nafion nanocomposite induced a modest improvement in hind limb locomotor recovery without inducing hyperalgesia. Conclusion These data suggest that the CNT/Nafion nanocomposite may be an effective material to promote axonal repair and regeneration after SCI.