Background Although the prevalence of head injury is estimated to be high in juveniles in prison, the extent of persisting disability is unknown and relationships with offending uncertain. This limited understanding makes it difficult to develop effective management strategies and interventions to improve health or reduce recidivism. This study investigates effects of significant head injury (SHI) on cognitive function, disability and offending in juvenile prisoners, and considers relationships with common comorbidities. Methods This cross-sectional study recruited male juvenile prisoners in Scotland from Her Majesty’s Young Offenders Institute (HMYOI) Polmont (detaining approximately 305 of 310 male juveniles in prison in Scotland). To be included juveniles had to be 16 years or older, fluent in English, able to participate in assessment, provide informed consent and not have a severe acute disorder of cognition or communication. Head injury, cognition, disability, history of abuse, mental health and problematic substance use were assessed by interview and questionnaire. Results We recruited 103 (34%) of 305 juvenile males in HMYOI Polmont. The sample was demographically representative of juvenile males in prisons for young offenders in Scotland. SHI was found in 82/103 (80%) and head injury repeated over long periods of time in 69/82 (85%). Disability was associated with SHI in 11/82 (13%) and was significantly associated with mental health problems, particularly anxiety. Group differences on cognitive tests were not found. However the SHI group reported poorer behavioural control on the Dysexecutive Questionnaire and were more often reported for incidents in prison than those without SHI. Characteristics of offending, including violence, did not differ between groups. Conclusions Although SHI is highly prevalent in juvenile prisoners, associated disability was relatively uncommon. There was no evidence for differences in cognitive test performance or offending in juveniles with and without SHI. However, signs of poorer behavioural control and greater psychological distress in juveniles with SHI suggest that they may be at greater risk of recidivism and of potentially becoming lifelong offenders. This implies a need for remedial programmes for juvenile prisoners to take account of persisting effects of SHI on mental health and self-control and education and to improve their understanding of the effects of SHI reduce the likelihood of cumulative effects from further SHI.