The aim of the present study was to quantify joint kinematics through a wearable sensor system in multidirectional high-speed complex movements used in a protocol for rehabilitation and return to sport assessment after Anterior Cruciate Ligament (ACL) injury, and to validate it against a gold standard optoelectronic marker-based system. Thirty-four healthy athletes were evaluated through a full-body wearable sensor (MTw Awinda, Xsens) and a marker-based optoelectronic (Vicon Nexus, Vicon) system during the execution of three tasks: drop jump, forward sprint, and 90° change of direction. Clinically relevant joint angles of lower limbs and trunk were compared through Pearson’s correlation coefficient (r), and the Coefficient of Multiple Correlation (CMC). An excellent agreement (r > 0.94, CMC > 0.96) was found for knee and hip sagittal plane kinematics in all the movements. A fair-to-excellent agreement was found for frontal (r 0.55–0.96, CMC 0.63–0.96) and transverse (r 0.45–0.84, CMC 0.59–0.90) plane kinematics. Movement complexity slightly affected the agreement between the systems. The system based on wearable sensors showed fair-to-excellent concurrent validity in the evaluation of the specific joint parameters commonly used in rehabilitation and return to sport assessment after ACL injury for complex movements. The ACL professionals could benefit from full-body wearable technology in the on-field rehabilitation of athletes.