Abstract Background Childhood obesity is one of the most critical and accelerating health challenges throughout the world. It is a major risk factor for developing varus/valgus misalignments of the knee joint. The combination of misalignment at the knee and excess body mass may result in increased joint stresses and damage to articular cartilage. A training programme, which aims at developing a more neutral alignment of the trunk and lower limbs during movement tasks may be able to reduce knee loading during locomotion. Despite the large number of guidelines for muscle strength training and neuromuscular exercises that exist, most are not specifically designed to target the obese children and adolescent demographic. Therefore, the aim of this study is to evaluate a training programme which combines strength and neuromuscular exercises specifically designed to the needs and limitations of obese children and adolescents and analyse the effects of the training programme from a biomechanical and clinical point of view. Methods/Design A single assessor-blinded, pre-test and post-test randomised controlled trial, with one control and one intervention group will be conducted with 48 boys and girls aged between 10 and 18 years. Intervention group participants will receive a 12-week neuromuscular and quadriceps/hip strength training programme. Three-dimensional (3D) gait analyses during level walking and stair climbing will be performed at baseline and follow-up sessions. The primary outcome parameters for this study will be the overall peak external frontal knee moment and impulse during walking. Secondary outcomes include the subscales of the Knee injury and Osteoarthritis Outcome Score (KOOS), frontal and sagittal kinematics and kinetics for the lower extremities during walking and stair climbing, ratings of change in knee-related well-being, pain and function and adherence to the training programme. In addition, the training programme will be evaulated from a clinical and health status perspective by including the following analyses: cardiopulmonary testing to quantify aerobic fitness effects, anthropometric measures, nutritional status and psychological status to characterise the study sample. Discussion The findings will help to determine whether a neuromuscular and strength training exercise programme for the obese children population can reduce joint loading during locomotion, and thereby decrease the possible risk of developing degenerative joint diseases later in adulthood. Trial registration ClinicalTrials NCT02545764 , Date of registration: 24 September 2015.