Brain computer interfaces (BCIs) using event-related desynchronization (ERD) of the electroencephalogram (EEG), which is believed to represent increased activation of the sensorimotor cortex, have attracted attention as tools for rehabilitation of upper limb motor functions in hemiplegic stroke patients. However, it remains unclear whether the corticospinal excitability is actually correlated with ERD. The purpose of this study was to assess the association between the ERD magnitude and the excitability of primary motor cortex (M1) and spinal motoneurons. M1 excitability was tested by motor evoked potentials (MEPs), short-interval intracortical inhibition (SICI) and intracortical facilitation (ICF) using transcranial magnetic stimulation, and spinal motoneuronal excitability was tested by F-waves using peripheral nerve stimulation. Results showed that large ERD during motor imagery was associated with significantly increased F-wave persistence and reduced SICI, but no significant changes in ICF and the response average of F-wave amplitudes. Our findings suggest that ERD magnitude during motor imagery represents the instantaneous excitability of both M1 and spinal motoneurons. This study provides electrophysiological evidence that ERD-based BCI with motor imagery task increases corticospinal excitability as changes accompanying actual movements.