Deception is a cognitive process in humans and animals which is not well understood. Most studies on lie detection have focused on emotional components associated with deception. We employed transcranial magnetic stimulation of the motor cortex in conjunction with a constrained question answer protocol for the first time to show increased cortical excitability in generating deceptive responses, in contrast with truthful responses. This may be due to increased cognitive activity in the motor and premotor connections. Our findings corroborate functional imaging studies and may have future implications in evaluating lie detection.