The aim of the present study was to predict the kinematics of the knee and the ankle joints during a squat training task of different intensities. Lower limb surface electromyographic (sEMG) signals and the 3-D kinematics of lower extremity joints were recorded from 19 body builders during squat training at four loading conditions. A long-short term memory (LSTM) was used to estimate the kinematics of the knee and the ankle joints. The accuracy, in terms root-mean-square error (RMSE) metric, of the LSTM network for the knee and ankle joints were 6.774 ± 1.197 and 6.961 ± 1.200, respectively. The LSTM network with inputs processed by cross-correlation (CC) method showed 3.8% and 4.7% better performance in the knee and ankle joints, respectively, compared to when the CC method was not used. Our results showed that in the prediction, regardless of the intensity of movement and inter-subject variability, an off-the-shelf LSTM decoder outperforms conventional fully connected neural networks.