Music is a form of sensory information with diverse preferences observed among individuals. These individual variations in music preferences can be attributed to individual differences in the neural processing of music. However, the specific neural processes responsible for such differences have not been specified, as the limitations of previous experimental designs in distinguishing between inter- and intra-individual preference variations. To address this issue, our study aimed to identify neural signals indicative of individual preference differences using univariate and multivariate analyses designed to assess inter-individual variations in neural signaling. In our experiments, we collected fMRI signals and preference ratings from participants while they listened to a range of music genres for over three hours. Our analysis identified specific brain regions in which there is a correlation between inter-individual variations in fMRI signals and preference ratings. We found a significant correlation mainly in a part of the planum temporale within both hemispheres, consistent across analytical methods. Meanwhile, we observed intra-individual correlations between fMRI signals and preference ratings in broader regions of the superior temporal cortex. Our findings suggest that inter-individual differences in music preferences are signaled within a confined area of the superior temporal cortex, distinct from the areas associated with intra-individual variations. These insights bring us significantly closer to understanding individuals’ music experiences in future research. The neuroscientific exploration of music preferences paves the way for tailored music experiences. Additionally, it opens avenues for innovative approaches in diverse music therapies.