This proposed study will examine whether structured physical activity reduces the recovery time of cognitive functioning during the early phase of substance use disorder treatment. Addiction or substance dependence is associated with neurobiological changes and cognitive impairment that can affect quality of life and the efficacy of therapy for up to a year after clinical detoxification. The biological, psychological, and social effects of physical exercise have the potential to be a therapeutic approach to increase quality of life and relieve symptoms associated with substance abuse, such as psychosis, depression, and anxiety. There is a dearth of research on physical activity and exercise in clinical substance use disorder patients. This protocol describes a clinical study that will examine cognitive recovery after substance abuse using physical exercise as a treatment intervention. We will use a quasi-experimental longitudinal clinical trial, with a pretest and multiple posttests, on naturally randomized sequential groups. Patients will be consecutively be recruited into the study groups, with a control group that is completed, before its followed by an intervention group, each with 30 patients. Patients will be enrolled 2 weeks after the start of detoxification, at which time all subjects will be inpatients at the Stavanger Salvation Army Treatment Center in the Norwegian specialized healthcare system. Cognition will be evaluated with a comprehensive battery of cognitive tests, including several tests of executive function. Physical fitness will be tested with the Rockport 1-Mile Walk Test, the 30-S Chair Stand Test, the 1-Min Burpee Test at baseline (within the first 2 weeks of admittance) and after 4 weeks. The intervention will be a 30-min workout at 70–90% of maximum heart rate (134–170 bpm), recorded and calculated by a Polar heart rate monitor. The intervention treatment will be administered four times a week for 4 weeks and will consist of high-intensity circuit training, high-intensity interval training, functional movement, and primitive reflex training. We anticipate improvement in both the control and intervention groups, with the exercise intervention group having the greatest increase in recovery of cognitive function because of the combination of functional full body movements and primitive movement training in an intense interval training program.