Shame and guilt are similar yet distinct self-conscious emotions that often facilitate the attainment of social goals and motivate behaviors that promote social acceptance. Recent studies have shown that individuals with autism or high autistic traits may tend to exhibit higher shame-proneness and lower guilt-proneness. This study examined whether this profile of self-conscious emotions can be explained by the functional organization of the brain using resting-state fMRI. Autistic traits, shame- and guilt-proneness and whole-brain resting-state fMRI data were measured in 45 neurotypical individuals. Our results revealed that the positive association between autistic traits and shame-proneness was mediated by resting-state functional connectivity between the right frontal pole and several regions among the cortical midline structures, including the precuneus, anterior cingulate and posterior cingulate. Additionally, functional connectivity between the right frontal pole and precuneus was found to mediate the negative association between autistic traits and guilt-proneness. These findings highlight the role of the cortical midline structures as a key neural substrate underlying differential experiences of negative self-conscious emotions among individuals with high autistic traits.