Human and animal studies suggest that both traumatic nerve injury and toxic challenge with chemotherapeutic agents involves the reorganization of neural circuits in the brain. However, there have been no prospective studies, human or animal, using magnetic resonance imaging (MRI) to identify changes in brain neural circuitry that accompany the development of chemotherapy-induced neuropathic pain (i.e. within days following cessation of chemotherapy treatment and without the confound cancer). To this end, different MRI protocols were used to ascertain whether a reorganization of brain neural circuits is observed in otherwise normal rats exposed to the taxane chemotherapeutic agent paclitaxel. We conducted an imaging study to evaluate the impact of a well-established paclitaxel dosing regimen, validated to induce allodynia in control rats within eight days of treatment, on brain neural circuitry. Rats received either paclitaxel (2 mg/kg/day i.p; cumulative dose of 8 mg/kg) or its vehicle four times on alternate days (i.e. day 0, 2, 4, 6). Following the cessation of treatments (i.e. on day 8), all rats were tested for responsiveness to cold followed by diffusion weighted magnetic resonance imaging and assessment of resting state functional connectivity. Imaging data were analyzed using a 3D MRI rat with 173 segmented and annotated brain areas. Paclitaxel-treated rats were more sensitive to a cold stimulus compared to controls. Diffusion weighted imaging identified brain areas involved in the emotional and motivational response to chronic pain that were impacted by paclitaxel treatment. Affected brain regions included the prefrontal cortex, amygdala, hippocampus, hypothalamus and the striatum/nucleus accumbens. This putative reorganization of gray matter microarchitecture formed a continuum of brain areas stretching from the basal medial/lateral forebrain to the midbrain. Resting state functional connectivity showed reorganization between the periaqueductal gray, a key node in nociceptive neural circuitry, and connections to the brainstem. Our results, employing different imaging modalities to assess the central nervous system effects of chemotherapy, fit the theory that chronic pain is regulated by emotion and motivation and influences activity in the periaqueductal gray and brainstem to modulate pain perception.