The purpose of this research was to determine if the commercially available Perception Neuron motion capture system was valid and reliable in clinically relevant lower limb functional tasks. Twenty healthy participants performed two sessions on different days: gait, squat, single-leg squat, side lunge, forward lunge, and counter-movement jump. Seven IMUs and an OptiTrack system were used to record the three-dimensional joint kinematics of the lower extremity. To evaluate the performance, the multiple correlation coefficient (CMC) and the root mean square error (RMSE) of the waveforms as well as the difference and intraclass correlation coefficient (ICC) of discrete parameters were calculated. In all tasks, the CMC revealed fair to excellent waveform similarity (0.47–0.99) and the RMSE was between 3.57° and 13.14°. The difference between discrete parameters was lower than 14.54°. The repeatability analysis of waveforms showed that the CMC was between 0.54 and 0.95 and the RMSE was less than 5° in the frontal and transverse planes. The ICC of all joint angles in the IMU was general to excellent (0.57–1). Our findings showed that the IMU system might be utilized to evaluate lower extremity 3D joint kinematics in functional motions.