Self-conscious emotions, such as shame and guilt, play a fundamental role in regulating moral behavior and in promoting the welfare of the society. Despite their relevance, the neural bases of these emotions are uncertain. In the present meta-analysis, we performed a systematic literature review in order to single out functional neuroimaging studies on healthy individuals specifically investigating the neural substrates of shame, embarrassment and guilt. Seventeen studies investigating the neural correlates of shame/embarrassment, and seventeen studies investigating guilt brain representation met our inclusion criteria. The analyses revealed that both guilt and shame/embarrassment were associated with the activation of the left anterior insula, involved in emotional awareness processing, and arousal. Guilt specific areas were located within the left temporo-parietal junction, which is thought to be involved in social cognitive processes. Moreover, specific activations for shame/embarrassment involved areas related to social pain (dorsal anterior cingulate, insula, thalamus), behavioral inhibition (premotor cortex) networks. This pattern of results might reflect distinct action tendencies associated with the two emotions.