Understanding others as intentional agents is critical in social interactions. We perceive others' intentions through identification, a categorical judgment that others should work like oneself. The most primitive form of understanding others' intentions is joint attention (JA). During JA, an initiator selects a shared object through gaze (initiative joint attention, IJA), and the responder follows the direction of the initiator's gaze (reactive joint attention, RJA). Therefore, both participants share the intention of object selection. However, the neural underpinning of shared intention through JA remains unknown. In this study, we hypothesized that JA is represented by inter-individual neural synchronization of the intention-related activity. Additionally, JA requires eye contact that activates the limbic mirror system; therefore, we hypothesized that this system is involved in shared attention through JA. To test these hypotheses, participants underwent hyperscanning fMRI while performing JA tasks. We found that IJA-related activation of the right anterior insular cortex of participants was positively correlated with RJA-related activation of homologous regions in their partners. This area was activated by volitional selection of the target during IJA. Therefore, identification with others by JA is likely accomplished by the shared intentionality of target selection represented by inter-individual synchronization of the right anterior insular cortex.