ObjectivesTo measure the clinical, structural and functional changes of an individualised structured cognitive rehabilitation in mild traumatic brain injury (mTBI) population.SettingA single centre study, Malaysia.ParticipantsAdults aged between 18 and 60 years with mTBI as a result of road traffic accident, with no previous history of head trauma, minimum of 9 years education and abnormal cognition at 3 months will be included. The exclusion criteria include pre-existing chronic illness or neurological/psychiatric condition, long-term medication that affects cognitive/psychological status, clinical evidence of substance intoxication at the time of injury and major polytrauma. Based on multiple estimated calculations, the minimum intended sample size is 50 participants (Cohen’s d effect size=0.35; alpha level of 0.05; 85% power to detect statistical significance; 40% attrition rate).InterventionsIntervention group will receive individualised structured cognitive rehabilitation. Control group will receive the best patient-centred care for attention disorders. Therapy frequency for both groups will be 1 hour per week for 12 weeks.Outcome measuresPrimary:Neuropsychological Assessment Battery-Screening Module (S-NAB) scores.Secondary:Diffusion Tensor Imaging (DTI) parameters and Goal Attainment Scaling score (GAS).ResultsResults will include descriptive statistics of population demographics, CogniPlus cognitive program and metacognitive strategies. The effect of intervention will be the effect size of S-NAB scores and mean GAS T scores. DTI parameters will be compared between groups via repeated measure analysis. Correlation analysis of outcome measures will be calculated using Pearson’s correlation coefficient.ConclusionThis is a complex clinical intervention with multiple outcome measures to provide a comprehensive evidence-based treatment model.Ethics and disseminationThe study protocol was approved by the Medical Research Ethics Committee UMMC (MREC ID NO: 2016928–4293). The findings of the trial will be disseminated through peer-reviewed journals and scientific conferences.Trial registration numberNCT03237676