Substance use is commonly associated with traumatic brain injury (TBI). We investigate associations between active substance use, peri-injury factors, and outcome after TBI across three U.S. Level I trauma centers. TBI subjects from the prospective Transforming Research and Clinical Knowledge in Traumatic Brain Injury Pilot (TRACK-TBI Pilot) with Marshall computed tomography (CT) score 1-3, no neurosurgical procedure/operation, and admission urine toxicology screen (tox+/-) were extracted. Associations between tox+/-, comorbidities, hospital variables, and six-month functional (GOSE) and neuropsychiatric (PCL-C, BSI18, RPQ-13, SWLS) outcomes were analyzed. Multivariable regression was performed for associations significant on univariate analysis with odds ratios (mOR) presented. Significance assessed at p textless 0.05. In 133 subjects, tox+/tox- were 29.1%/72.9%. Tox+ was younger (35.5/43.6-years, p = 0.018), trended toward male sex (80.6%/63.9%, p = 0.067), was associated with history of seizures (27.8%/10.3%, p = 0.012), self-reported substance use (44.4%/17.5%, p = 0.001), prior TBI (58.8%/34.1%, p = 0.009), GCS textless 15 (69.4%/48.4%, p = 0.031) and blood alcohol level textgreater0.08-mg/dl (55.6%/30.8%, p = 0.022). In CT-negative subjects, tox+ was associated with increased hospital admission (95.7%/66.7%, p = 0.034). At six-months, tox+ was associated with screening positive for post-traumatic stress disorder (PCL-C: 40.0%/15.9%; mOR = 8.24, p = 0.022) and psychiatric symptoms (BSI18: 40.0%/14.3%, mOR = 11.06, p = 0.023). Active substance use in TBI may confound GCS assessment, triage to higher level of care, and be associated with increased six-month neuropsychiatric symptoms. Substance use screening should be integrated into standard emergency/acute care TBI protocols to optimize management and resource utilization. Clinicians should be vigilant in providing education, counselling, and follow-up for TBI patients with substance use.