Investigating sex differences in various functional areas of the human brain is a prevalent and unresolved issue in understanding the brain’s operating mechanisms. This research examines sex differences using Univariate and Two-way Analysis on novel fMRI data obtained with music stimuli. This study proposes a method to distinguish sex differences from individual differences and uses nonparametric statistical tests to confirm the presence of sex differences, thereby validating the method. With our proposed methodology, we found more significant functional connectivity links between the hemispheres of the female brain than in the male brain. Moreover, the male brain responds to music stimuli more than the female. Finally, we uncovered that functional regions unrelated to hearing are highly active, highlighting the role of gender differences. It is predominantly found that the posterior cingulate cortex(PCC) shows high correlations in response to music stimulation in both genders. An in-depth exploration of the PCC’s dominant role in sex differences is expected to significantly contribute to research related to targeting areas of the human brain that dominate sex differences.