Mouth breathing can occur due to obstructive, habitual, or anatomical factors, and it causes various side effects such as decreased blood oxygen saturation, respiratory diseases, skeletal disorders in the facial area, decreased concentration, and sleep disorders. However, previous studies on these side effects of mouth breathing have mainly focused on structural changes. Because oxygen and glucose are essential for brain metabolism, studies on their changes due to mouth breathing have been required. Therefore, this study was to investigate the activation of brain regions during different types of breathing (nasal and mouth breathing) using fluorodeoxyglucose (FDG) positron emission tomography (PET) and blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI). FDG-PET and BOLD-fMRI data were obtained from ten healthy subjects. Image pre-processing and group analysis were conducted using statistical parametric mapping (SPM12). FDG-PET showed that cerebral areas, such as middle frontal, superior and inferior parietal and inferior frontal gyrus, were highly active during nasal breathing and that the cerebellar areas were highly active during mouth breathing. BOLD-fMRI showed that the inferior occipital and the superior frontal gyrus, and the gyrus rectus were highly active during nasal breathing. This study confirmed that mouth breathing interferes with the normal functioning of the cerebrum, such as its metabolism, thereby reducing the activations of the olfactory, autonomic nervous system, as well as the default mode network. These, along with structural changes, may cause deteriorations in brain functions.