To determine the associations between trauma variables, acute phase-related variables, and patient-level characteristics with functional recovery during inpatient rehabilitation for individuals with spinal cord injury (SCI). The associations were evaluated by linking individuals' records between the Pennsylvania Trauma Systems Outcomes Study and the National SCI Model Systems databases. Retrospective cohort analysis. Two SCI Model Centers in Pennsylvania, United States. We used a record linkage toolkit in Python to link 735 individuals with traumatic SCI between the databases. The percentage for true-match and error were 92.0% and 0.1%, respectively. The functional recovery during inpatient rehabilitation was determined in 604 individuals with SCI by ordinary least squares regression (OLS) and gradient boosting regression (GBR) analyses. The OLS and GBR analyses indicated older age, greater impairment (SCI level combined with American Spinal Injury Association impairment scale), presence of diabetes mellitus, pulmonary complications during acute care, and longer length of stay at an inpatient rehabilitation facility were associated with lower functional recovery (OLS R 2  = 0.56 and GBR R 2  = 0.58). Trauma and acute care variables in addition to patient characteristics were associated with functional recovery during inpatient rehabilitation in individuals with SCI. Further investigation is needed to understand the role of diabetes mellitus and pulmonary complications, which have not been previously associated with functional recovery in individuals with SCI.