Rehabilitation is a hazardous task for a mechanical system, since the device has to interact with the human extremities without the hands-on experience the physiotherapist acquires over time. A gap needs to be filled in terms of designing effective controllers for this type of devices. In this respect, the paper describes the design of a model-based control for an electromechanical lower-limb rehabilitation system based on a parallel kinematic mechanism. A controller–observer was designed for estimating joint velocities, which are then used in a hybrid position/force control scheme. The model parameters are identified by customising an approach based on identifying only the relevant system dynamics parameters. Findings obtained through simulations show evidence of improvement in tracking performance compared with those where the velocity was estimated by numerical differentiation. The controller is also implemented in an actual electromechanical system for lower-limb rehabilitation tasks. Findings based on rehabilitation tasks confirm the findings from simulations.