Immature cognition is susceptible to interference from competing information, and particularly in affectively charged situations. Several studies have reported activation in the anterior cingulate cortex, prefrontal cortex and amygdala associated with emotional conflict processing in adults but literature is lacking regarding children. Moreover, studies in children and adolescents still disagree regarding the functional activation of amygdala related to facial stimuli. In the purpose of investigating both the effect of socio-emotional stimuli and its interaction with interference control, we designed a flanker task associated with an event-related fMRI paradigm in 30 healthy children ages 9-11. In addition to happy, angry and neutral faces, we presented scrambled stimuli to examine a potential effect of faces. Regarding both brain and behavior results, no effect of emotional valence was observed. However, both results evidenced an emotional effect of faces compared with scrambled stimuli. This was expressed by faster RTs associated with increased amygdala activity and activation of the ventral ACC, in congruent trials only. When scrambled were inversely compared to faces, increased activity was observed within the lateral prefrontal cortex. Regarding the amygdala, the results suggest that in late school age children, activity in the amygdala seemed to underlie the socio-emotional effect induced by faces but not the emotional conflict. Studying brain regions involved in emotion regulation is important to further understand neurodevelopmental disorders and psychopathologies, particularly in late childhood and adolescence.