Delivering short trains of electric pulses to the muscles and nerves can elicit action potentials resulting in muscle contractions. When the stimulations are sequenced to generate functional movements, such as grasping or walking, the application is referred to as functional electrical stimulation (FES). Implications of the motor and sensory recruitment of muscles using FES go beyond simple contraction of muscles. Evidence suggests that FES can induce short- and long-term neurophysiological changes in the central nervous system by varying the stimulation parameters and delivery methods. By taking advantage of this, FES has been used to restore voluntary movement in individuals with neurological injuries with a technique called FES therapy (FEST). However, long-lasting cortical re-organization (neuroplasticity) depends on the ability to synchronize the descending (voluntary) commands and the successful execution of the intended task using a FES. Brain-computer interface (BCI) technologies offer a way to synchronize cortical commands and movements generated by FES, which can be advantageous for inducing neuroplasticity. Therefore, the aim of this review paper is to discuss the neurophysiological mechanisms of electrical stimulation of muscles and nerves and how BCI-controlled FES can be used in rehabilitation to improve motor function.