Pain is a pervasive problem that affects nearly half of the U.S. Veterans deployed in support of the Global War on Terror (Post-9/11 Veterans) and over half of the Post-9/11 Veterans with diagnosed traumatic brain injury (TBI). The goal of the current study was to identify pain phenotypes based on distinct longitudinal patterns of pain scores in light of pain treatment among Post-9/11 Veterans over five years of care using latent growth mixture analysis stratified by TBI status. Five pain phenotypes emerged: (1) simple low impact stable pain, (2) complex low impact stable pain, (3) complex low impact worsening pain, (4) complex moderate impact worsening pain, and (5) complex high impact stable pain. Baseline pain scores and slopes were significantly higher in Veterans with mild TBI for some phenotypes. The mild TBI cohort was younger, had more men, more whites, less blacks, less education, more unmarried, more Marines and Army, more active duty in comparison to the no TBI cohort. Distinct trajectories in pain treatment were apparent among the pain intensity subgroups. Perspective: The complexity of pain in patients with mTBI is categorically different than those with no TBI. Pain in patients with mTBI is heterogeneous with distinct phenotypes which may explain poor outcomes in this group. Identification of the individual differences may have a significant impact on the success of interventions.