Although it represents the most potent toxin known to humanity, botulinum toxin type A (BT-A) has found its place over the last 30 years in the therapy of various conditions accompanied by muscle hypercontractility. Recent studies have indicated its antinociceptive effect, with the first case of approval as treatment for chronic migraine. Besides migraine, it shows great potential in the therapy of various types of neuropathic pain. In addition to therapeutic use, it has also become an indispensable part of modern aesthetic medicine and one of the most popular aesthetic procedures, generally being accepted as safe and without serious adverse side effects. Evidence of BT-A's trans-synaptic transport in the visual, motor, and sensory systems has further confirmed the hypothesis of a central mechanism of action on pain, given that BT-A reaches the first synapse within the spinal cord through retroaxonal transport from the periphery, where it interferes with various neurotransmitter systems. Therefore, the question arises whether BT-A remains at the spinal cord level or is transported trans-synaptically to supraspinal regions. The aim of this research was to examine the distribution of BT-A within the hypothalamus, hippocampus, gracile, and facial nuclei after unilateral peripheral administration to the hind paw of rats. The immunohistochemical method tracked an indirect indicator of BT-A proteolytic activity, the cleaved fragment of the SNAP-25 protein. The signal of cleaved SNAP-25 was detected within all observed regions, with a reduction in signal intensity noted in the group treated with a specific antitoxin for BT-A. This effect is the result of the neutralization of a part of extracellular BT-A by the antitoxin and an indirect proof of BT-A trans-synaptic transport in the central nervous system. The presented results raise numerous questions about the significance of these findings, especially in the context of the safety of long-term BT-A use, and require further investigation.