Background The anterior cingulate cortex (ACC) has been shown to be involved in emotional distress induced by social exclusion and the ventrolateral prefrontal cortex (VLPFC) in the regulation or inhibition of the distress. Here, we examined modulation of effective connectivity between the regions in response to emotional feedback in children with experiences of ostracism in their everyday life. Methods In functional magnetic resonance imaging experiments, 10 ostracized children and 11 control children were provided emotional feedback inducing negative or positive affective states. We employed effective connectivity analysis to explore connectivity models comprising the VLPFC and ACC, and to estimate connectivity parameters over the models. Results In spite of psychological impacts on the ostracized children, behavioral data showed that their emotional responses did not deviate from the control children in response to the emotional feedback. The VLPFC to ACC connectivity was modulated only in the ostracized children, such that the modulation may help them regulate their emotional responses. Conclusions The findings suggest that the effects of ostracism experiences on affective processing can be revealed in terms of modulation of prefrontal‐cingulate connectivity.