Mal de debarquement syndrome (MdDS) is a chronic disorder of imbalance characterized by a feeling of rocking and swaying. The medical treatment for MdDS is still limited. Motivated by our previous pilot study that demonstrates the promising clinical efficacy of repetitive transcranial stimulation (rTMS) in MdDS patients, a novel rTMS paradigm, i.e., 1 Hz stimulation over ipsilateral dorsal lateral prefrontal cortex (DLPFC) with respect to the dominant hand followed by 10 Hz stimulation over contralateral DLPFC, was proposed and conducted in MdDS in the present study. To evaluate the potential efficacy, we examined the changes before and after rTMS in both subjective reported symptom using visual analogue scale (VAS) and direct brain activity in resting state electroencephalography (rsEEG). To disentangle activity from distinct brain substrates and/or local networks in rsEEG signals, a group-wise independent component analysis was employed and the corresponding spectral power changes were examined in the identified components. In general, reduction in rocking sensation was reported in five of ten subjects (with dramatic reductions (changes > 30) in three subjects) after rTMS using the present paradigm, while no changes and slight increases in rocking sensation were reported in the remaining subjects. In rsEEG, significant elevated spectral powers in low frequency bands (i.e., theta and alpha) over broad areas of occipital, parietal, motor, and prefrontal cortices were induced by rTMS, reflecting the enhancement of cortical inhibition over these areas. Meanwhile, the significant correlations between changes in rsEEG and VAS scores were detected in the high frequency bands (i.e., high alpha and beta) over posterior parietal and left visual areas, reflecting the suppression of spatial information processing. Therefore, the present findings demonstrate the promising clinical efficacy of a new rTMS paradigm for MdDS, and suggest its merit for further studies in more patients.