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Traumatic Brain Injuries (TBI) can lead to behavioral difficulties that increase the risk of interaction with the criminal justice system. Using a neurocriminology framework, this study investigated neurological anomalies as a predictor of custodial challenges in Rikers Island, New York City Jail. The sample included 16-18 year old detainees. Using a mixed method design, health and criminal justice data provided by New York City Department of Health and Mental Hygiene were examined (N=262), and in-depth inmate interviews were conducted and analyzed (N=20). A 50% prevalence of pre-existing TBI was identified with 34% occurring from community violence. TBI-inmates had greater mental health needs (OR =1.95, p<0.05), were in custody longer (OR = 1.07, p<0.01), and spent more time in punitive segregation (OR=1.91 p<0.05). Qualitative analyses added that TBI-inmates experienced more fights and weapons-related injuries, and faced unique challenges in punitive segregation including self-injury or suicide attempts, food deprivation, and claustrophobia. TBI education and training for staff and inmates could improve correctional and health management. Ongoing TBI screening and assessment can inform appropriate custodial programming, court practices, and reentry planning. Increased community awareness through schools and healthcare providers is essential for prevention and adequate care of TBIs.