Relational victimization typically emerges first during the elementary school period, and has been associated with increased levels of internalizing symptoms in children. Individual differences in autonomic nervous system functioning have been suggested as a potential factor linking social stressors and internalizing symptoms. The aim of this study was therefore to examine whether heart rate and heart rate variability mediated the association between relational victimization and internalizing symptoms in 373 mainstream elementary school children. Children were assessed in 2015 (T0; Grades 3–5, M age = 9.78 years, 51% boys) and reassessed in 2016 (T1). Heart rate and heart rate variability were assessed during a regular school day at T1. A multi-informant (teacher and peer report) cross-time measure of relational victimization, and a multi-informant (self- and teacher report) measure of internalizing problems at T1 was used. Results showed that heart rate variability, but not heart rate, mediated the association between relational victimization and internalizing symptoms. This study provides tentative support that in children from a general population sample, a psychobiological factor may mediate the association of relational victimization with internalizing symptoms.