Movement analysis of human body parts is momentous in several applications including clinical diagnosis and rehabilitation programs. The objective of this research is to present a low-cost 3D visual tracking system to analyze the movement of various body parts during therapeutic procedures. Specifically, a marker based motion tracking system is proposed in this paper to capture the movement information in home-based rehabilitation. Different color markers are attached to the desired joints’ locations and they are detected and tracked in the video to encode their motion information. The availability of this motion information of different body parts during the therapy can be exploited to achieve more accurate results with better clinical insight, which in turn can help improve the therapeutic decision making. The proposed framework is an automated and inexpensive motion tracking system with execution speed close to real time. The performance of the proposed method is evaluated on a dataset of 10 patients using two challenging matrices that measure the average accuracy by estimating the joints’ locations and rotations. The experimental evaluation and its comparison with the existing state-of-the-art techniques reveals the efficiency of the proposed method.