Childhood maltreatment and peer victimisation are common sources of early-life interpersonal stress. Childhood maltreatment is associated with atypical frontolimbic emotion processing and regulation, and increased vulnerability for self-harm/suicide. However, few studies have compared the neurofunctional correlates between caregiver- versus peer-inflicted mistreatment. We compared the alterations of neurofunctional correlates of facial emotion processing in youths exposed to childhood maltreatment or peer victimisation, and explored their associations with self-harm. Functional magnetic resonance imaging data were collected from 114 age- and gender-matched youths (39 childhood maltreatment, 37 peer victimisation and 38 controls) during an emotion discrimination task. Region-of-interest (amygdala, insula) and whole-brain analyses were conducted. Groups differed significantly during disgust processing only. Both groups had lower activation in the right amygdala and bilateral posterior insula than controls; left insular underactivation was furthermore related to increased self-harm in maltreated youths. Compared with controls, at the whole-brain level, both groups also had underactivation in a cluster of bilateral limbic-thalamic-striatal, precuneus/posterior cingulate, temporal, fusiform/lingual and cerebellar regions, which was negatively associated with emotional problems in controls, as well as a cluster of somatosensory regions associated with increased self-harm in maltreated youths. Early-life interpersonal stress from caregivers or peers is associated with common underactivation of limbic-thalamic-striatal, precuneus/posterior cingulate and somatosensory regions during disgust processing. The hypoactivation of key emotion and sensory processing and self-referential brain regions could be a potential suppressive mechanism to cope with the aversive emotion; however, it may also entail increased risk of affective psychopathology in seemingly healthy youths.