Three-dimensional (3D) motion analysis (MA) techniques are progressively being used in biomechanics research and for clinical applications to assess the risk of injuries. A marker-based 3D MA protocol has been developed to measure the upper and lower extremity (UE and LE) joints’ active and passive ranges of motion (AROM and PROM) in children. The joints that were included in this protocol are shoulder, elbow, wrist, hip, knee and ankle. The anatomical joint coordinate systems (JCS) have been defined for the upper and lower extremities to standardize reporting. A marker placement model was defined according to the International Society of Biomechanics (ISB) recommendations and used to develop the protocol. The proposed movements will be captured and analyzed using the Motion Analysis Corporations 3D MA system integrated with Cortex software. The movements adopted in this study have been selected from various sources to incorporate all joint rotations while ensuring the isolation of each joint motion during the movements. It is recommended that future studies utilize this protocol to draw a relationship between the joints’ range of motion (ROM) and the adjacent segments characteristics, i.e., segment length, joint stiffness, etc.