There is an increase of inactivity and overweight in children and adolescents which has a negative impact on their physical, motoric, emotional and cognitive development. This study examines changes in physical fitness and psychological well-being after participation in an intervention program offering a weekly professionally guided judo practice especially for overweight and obese children and adolescents. 26 overweight or obese children and adolescents (age 7 - 14) completed on average 28 sessions of judo training over a course of 12 months. Subjects completed a physical examination (stability, body composition, leg strength) and an assessment of psychological well-being (health-related quality of life, mental health problems) prior to entering the study, after 6 months and after completion of the training. We found significant changes in stability (p < .001), fat free mass (p = .001), leg strength (left p = .022, right p = .019), mental health problems (p < .001), conduct problems (p < .001) and peer problems (p < .001) and a trend in health-related quality of life (p = .055). Participants that dropped out (n = 12) showed a significantly higher BMI (p = .018) and higher scores in peer problems (p = .004). This study indicates that judo practice could have an influence on physical and psychological variables in overweight and obese children and adolescents. Judo provides a way to introduce regular physical activity among overweight and obese children and adolescents to support a more active lifestyle. We observed significant changes in physical fitness and psychological well-being in obese children after one year of judo practice. Approaches to support obese children in developing a more active lifestyle are of great significance.