Stroke is the leading cause of permanent disability in developed countries; its effects may include sensory, motor, and cognitive impairment as well as a reduced ability to perform self-care and participate in social and community activities. A number of studies have shown that the use of robotic systems in upper limb motor rehabilitation programs provides safe and intensive treatment to patients with motor impairments because of a neurological injury. Furthermore, robot-aided therapy was shown to be well accepted and tolerated by all patients; however, it is not known whether a specific robot-aided rehabilitation can induce beneficial cortical plasticity in stroke patients. Here, we present a procedure to study neural underpinning of robot-aided upper limb rehabilitation in stroke patients. Neurophysiological recordings use the following: (a) 10–20 system electroencephalographic (EEG) electrode montage; (b) bipolar vertical and horizontal electrooculographies; and (c) bipolar electromyography from the operating upper limb. Behavior monitoring includes the following: (a) clinical data and (b) kinematic and dynamic of the operant upper limb movements. Experimental conditions include the following: (a) resting state eyes closed and eyes open, and (b) robotic rehabilitation task (maximum 80 s each block to reach 4-min EEG data; interblock pause of 1 min). The data collection is performed before and after a program of 30 daily rehabilitation sessions. EEG markers include the following: (a) EEG power density in the eyes-closed condition; (b) reactivity of EEG power density to eyes opening; and (c) reactivity of EEG power density to robotic rehabilitation task. The above procedure was tested on a subacute patient (29 poststroke days) and on a chronic patient (21 poststroke months). After the rehabilitation program, we observed (a) improved clinical condition; (b) improved performance during the robotic task; (c) reduced delta rhythms (1–4 Hz) and increased alpha rhythms (8–12 Hz) during the resting state eyes-closed condition; (d) increased alpha desynchronization to eyes opening; and (e) decreased alpha desynchronization during the robotic rehabilitation task. We conclude that the present procedure is suitable for evaluation of the neural underpinning of robot-aided upper limb rehabilitation.