Neuroimaging biomarkers could offer more objective measures of the pain experience. This study investigated rT1/T2 maps of the brain as a novel biomarker for chronic pain in patients with central post-stroke pain (PSP) and persistent spinal pain syndrome type 2 (PSPS-II). Patients with PSP and PSPS-II were retrospectively included alongside healthy controls. Bias correction and intensity normalization were applied to the T1-weighted and T2-weighted images to generate the rT1/T2 maps of the brain. Subsequently, rT1/T2 maps were spatially correlated with neurotransmitter atlases derived from molecular imaging. In total, 15 PSPS-II patients, 11 PSP patients, and 18 healthy controls were included. No significant differences between patient and control demographics were found. Significant decreases in rT1/T2 signal intensity ( < 0.001) were observed in the dorsal and medial part of the thalamus, left caudate nucleus, cuneus, superior frontal gyrus, and dorsal cervicomedullary junction in PSP patients. No significant changes were found in rT1/T2 signal intensity in PSPS-II patients. Significant correlations were found with CB1-, 5HT2a-, and mGluR5-receptor maps (pFDR = 0.003, 0.030, and 0.030, respectively) for the PSP patients and with CB1-, 5HT1a-, 5HT2a-, KappaOp-, and mGluR5-receptor maps (pFDR = 0.003, 0.002, 0.002, 0.003, and 0.002, respectively) in PSPS-II patients. These findings suggest that microstructural alterations occur in the thalamus, cuneus, and dorsal cervicomedullary junction in patients with PSP. The lack of significant findings in rT1/T2 in PSPS-II patients combined with the significant correlations with multiple neurotransmitter maps suggests varying degrees of microstructural deterioration in both chronic pain syndromes, although further research is warranted.