Shame and guilt are moral emotions that play an important role in social functioning. There is limited knowledge about the neural underpinnings of these emotions, particularly in young people. In the current study, 36 healthy females (mean age 18.8 ± 1.9 years) underwent functional Magnetic Resonance Imaging, during which they reflected on their decisions about social moral dilemmas, and subsequently received negative or positive peer feedback. Ratings of shame and guilt were used as parametric modulators of brain activity. Shame was associated with decreased activity in the superior temporal sulcus and precentral gyrus during reflection. Guilt was associated with decreased activity in the precuneus during positive feedback, and in the hippocampus and supramarginal gyrus during negative feedback. Results suggest that shame and guilt are associated with activity in brain regions involved in social cognition and emotion regulation; however, they have distinct underlying neural circuitry that may be differentiated based on social evaluation.