Background: Executive dysfunction appears to be related to increased recidivism. Of note is that sleep disturbances, which are highly prevalent in prisons, may attenuate executive functions. Thus, improving executive functions, either directly or indirectly through the improvement of sleep, may reduce recidivism. It is hypothesised that physical exercise, in the form of Running Therapy, has a direct positive effect on executive functions as well as an indirect effect through the improvement of sleep. Methods/Design: Seventy two (N = 72) detainees in various penitentiary institutions in the Netherlands will be recruited in this study. A baseline measurement, including six neuropsychological tests of the Cambridge Neuropsychological Test Automated Battery (CANTAB), an assessment of sleep quality and duration using the Actiwatch (Actiwatch 2, Philips Respironics, Murrysville, PA, USA) and various other measurements will be administered before the start of the treatment. After 3 months of Running Therapy, participants will be assessed again with the same tests for neuropsychological and physical functioning. Primary outcomes are executive functioning and various sleep variables. Discussion: This study will be the first to investigate the possible influence of Running Therapy on the cognitive functioning, sleep and aggression in prisoners.