To develop a more reliable brain-computer interface (BCI) for patients in the completely locked-in state (CLIS), here we propose a Pavlovian conditioning paradigm using galvanic vestibular stimulation (GVS), which can induce a strong sensation of equilibrium distortion in individuals. We hypothesized that associating two different sensations caused by two-directional GVS with the thoughts of “yes” and “no” by individuals would enable us to emphasize the differences in brain activity associated with the thoughts of yes and no, and hence help us better distinguish the two from electroencephalography (EEG). We tested this hypothesis with 11 healthy and one CLIS participant. Our results showed that, first, conditioning of GVS with the thoughts of yes and no is possible. And second, the classification of whether an individual is thinking “yes” or “no” is significantly improved post conditioning, even in the absence of subsequent GVS stimulations. We observed average classification accuracy of 73.0% over 11 healthy individuals and 85.3% with the CLIS patient. These results suggest the establishment of GVS-based Pavlovian conditioning and its usability as a non-invasive BCI.