Objective: The Rubber Hand Illusion (RHI) manipulates body ownership experimentally and helps investigate the related neurophysiological processes. This study aimed to evaluate motor cortex excitability that hypothesized changed due to illusion. Method: Twenty-one healthy (twelve male, nine female), right-handed volunteers aged between 25 and 50 years were recruited to the study. Short-Latency Afferent Inhibition (SAI) was evaluated by transcranial magnetic stimulation (TMS) given with a figure-of-eight-shaped coil from the left motor cortex, 21 ms after peripheral electrical stimulation. Short-Interval Intracortical Inhibition (SICI) and Intracortical Facilitation (ICF) were investigated using a paired-pulse TMS at interstimulus intervals (ISI) of 1, 2.5, 3 ms and 15, 20, 25 ms, respectively. We used custom-made illusion setups for TMS paradigms. SAI, SICI and ICF was evaluated before, during and 15 min after the RHI. Results: Results of the study revealed significantly high SAI during illusion compared to pre-illusion, but no difference was found between post-illusion 15th minutes and control measurements. Significantly reduced SICI at 2.5 and 3 ms ISI obtained during illusion, while RHI did not affect SICI at 1 ms ISI and ICF. Significance: Body ownership illusion modulates the motor cortex excitability, possibly through altered sensory processing and sensorimotor integration.