As part of an investigation to detect asymmetries in gait patterns in persons with shoulder injuries, the goal of the present study was to design and validate a Kinect-based motion capture system that would enable the extraction of joint kinematics curves during gait and to compare them with the data obtained through a commercial motion capture system. The study included eight male and two female participants, all diagnosed with anterolateral shoulder pain syndrome in their right upper extremity with a minimum 18 months of disorder evolution. The participants had an average age of 31.8 ± 9.8 years, a height of 173 ± 18 cm, and a weight of 81 ± 15 kg. The gait kinematics were sampled simultaneously with the new system and the Clinical 3DMA system. Shoulder, elbow, hip, and knee kinematics were compared between systems for the pathological and non-pathological sides using repeated measures ANOVA and 1D statistical parametric mapping. For most variables, no significant difference was found between systems. Evidence of a significant difference between the newly developed system and the commercial system was found for knee flexion–extension (p < 0.004, between 60 and 80% of the gait cycle), and for shoulder abduction–adduction. The good concurrent validity of the new Kinect-based motion analysis system found in this study opens promising perspectives for clinical motion tracking using an affordable and simple system.