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Background: This study explored the relationship between history of substance abuse and pain severity during inpatient rehabilitation following traumatic spinal cord injury (SCI). Methods: Secondary analysis of a prospective longitudinal study. An adjusted general linear model was used to examine differences in functional improvement based on history of substance abuse and pain severity. Results: Over 50% of the sample had a history of substance abuse, and 94% reported moderate or severe pain. There was a significant interaction between the history of substance abuse and pain severity ( p  = 0.01, partial η 2 = 0.012). A difference in functional improvement was found among individuals who reported low pain; those with a history of substance abuse achieved less functional improvement than those without a history of substance abuse, M  = 5.32, SE  = 1.95, 95% CI 0.64-10.01. Conclusions: A history of substance abuse and post-injury pain are prevalent among individuals with SCI in rehabilitation, and there may be a meaningful relationship between these two patient characteristics and functional improvement. The results provide potential new insights into the characteristics of vulnerable subpopulations during SCI rehabilitation. Furthering our understanding of these results warrants future investigation to prevent and minimize poor outcomes among vulnerable SCI patients.