The response of trauma systems in rural areas is uncertain since distances between injury scenes and trauma care are considerable. Timely arrival at definitive care is critical for persons with traumatic brain injury (TBI) since secondary damage can occur during the hours following injury. We evaluated how the implementation of a trauma system in a predominately rural state affected the triage of TBI patients and their risk for mortality. The Iowa System Trauma Registry Dataset was analyzed, and included patients evaluated before trauma system implementation, 1997-1998, and after implementation, 2002-2003. Patients were identified using ICD9-CM codes or AIS codes, and included 710 pre-system patients and 886 post-system patients. Multivariate logistic regression assessed the effect of the trauma system on survival while controlling for confounders. Following implementation of the trauma system, patients treated in Level I or II facilities were older (p = 0.019), more often had multiple injuries (p = 0.0002), and had more severe TBI (p = 0.008). After controlling for confounders, transferred patients and those directly admitted were less likely to die in 72 h in the post-system than the pre-system (odds ratio [OR] = 0.56, 95% confidence interval (CI) = 0.36, 0.88; OR = 0.50, 95% CI = 0.32, 0.79). Implementation of the Iowa trauma system seems to have led to more appropriate triage and transport for TBI patients, and this likely contributed to reduced in-hospital mortality.