Substance use disorder is a worldwide issue that entails negative health and physical activity is a promising complementary therapy for alleviating the consequences. The objective of this reviews is to characterize physical activity interventions offered in the literature and explore their effects during treatment for people with substance use disorders with excluding studies focusing only on tobacco use. A systematic search of seven databases on articles including a physical activity intervention during a treatment for substance use disorder was done and an examination of the presence of bias was performed. A total of 43 articles including 3135 participants were identified. Most studies were randomized controlled trial (81%), followed by pre-post design (14%) and cohort studies (5%). The most common physical activity intervention identified was of moderate intensity, 3 times per week (≈ 1 hour) for 13 weeks. Cessation/reduction of substance use was the most studied outcome (21 studies, 49%), and 75% showed a decrease in substance use following physical activity intervention. Aerobic capacity was the second most studied effect (14 studies, 33%), with more than 71% of studies showing improvement. Twelve studies (28%) reported a decrease of depressive symptoms. Physical activity interventions in a treatment for substance use disorder seem to be a promising, but more methodologically rigorous scientific studies are needed.