Fear of movement-related pain is known to disturb the process of motor preparation in patients with chronic pain. In the present study, we aimed to clarify the neural mechanisms underlying the influence of fear movement-related pain on motor preparatory brain activity using Libet's clock and electroencephalography (EEG). Healthy participants were asked to press a button while watching a rotating Libet's clock-hand, and report the number on the clock ("W time") when they made the "decision" to press the button with their right index finger. Immediately after pressing the button, a painful electrical stimulus was delivered to the dorsum of the left hand, causing participants to feel fear of movement (button press-related pain). We found that fear of movement-related pain caused the W time to be early, and that the amplitudes of readiness potentials (RPs) increased after awareness of motor intention emerged. In addition, fear of movement-related pain caused over-activation of the medial frontal cortex, supplementary motor area, cingulate motor area, and primary motor cortex after participants became aware of their motor intention. Such over-activation might result from conflict between the unrealized desire to escape from a painful experience and motivation to perform a required motor task.