Flexible-joint manipulators are frequently used for increased safety during human-robot collaboration and shared workspace tasks. However, joint flexibility significantly reduces the accuracy of motion, especially at high velocities and with inexpensive actuators. In this paper, we present a learningbased approach to identify the unknown dynamics of a flexiblejoint manipulator and improve the trajectory tracking at high velocities. We propose a two-stage model which is composed of a one-step forward dynamics future predictor and an inverse dynamics estimator. The second part is based on linear timeinvariant dynamical operators to approximate the feed-forward joint position and velocity commands. We train the model endto-end on real-world data and evaluate it on the Baxter robot.Our experiments indicate that augmenting the input with onestep future state prediction improves the performance, compared to the same model without prediction. We compare joint position, joint velocity and end-effector position tracking accuracy against the classical baseline controller and several simpler models.