Brain–computer interface (BCI) is a novel communication method between brain and machine. It enables signals from the human brain to influence or control external devices. Currently, much research interest is focused on the BCI-based neural rehabilitation of patients with motor and cognitive diseases. Over the decades, BCI has become an alternative treatment for motor and cognitive rehabilitation. Previous studies demonstrated the usefulness of BCI intervention in restoring motor function and recovery of the damaged brain. Electroencephalogram (EEG)-based BCI intervention could cast light on the mechanisms underlying neuroplasticity during upper limb recovery by providing feedback to the damaged brain. BCI could act as a useful tool to aid patients with daily communication and basic movement in severe motor loss cases like amyotrophic lateral sclerosis (ALS). Furthermore, recent findings have reported the therapeutic efficacy of BCI in people suffering from other diseases with different levels of motor impairment such as spastic cerebral palsy, neuropathic pain, etc. Besides motor functional recovery, BCI also plays its role in improving the behavior of patients with cognitive diseases like attention-deficit/hyperactivity disorder (ADHD). The BCI-based neurofeedback training is focused on either reducing the ratio of theta and beta rhythm, or enabling the patients to regulate their own slow cortical potentials, and both have made progress in increasing attention and alertness. With summary of several clinical studies with strong evidence, we present cutting edge results from the clinical application of BCI in motor and cognitive diseases, including stroke, spinal cord injury, ALS, and ADHD.