One may have experienced his or her footsteps unconsciously synchronize with the footsteps of a friend while walking together, or heard an audience's clapping hands naturally synchronize into a steady rhythm. However, the mechanisms of body movement synchrony and the role of this phenomenon in implicit interpersonal interactions remain unclear. We aimed to evaluate unconscious body movement synchrony changes as an index of implicit interpersonal interaction between the participants, and also to assess the underlying neural correlates and functional connectivity among and within the brain regions. We found that synchrony of both fingertip movement and neural activity between the two participants increased after cooperative interaction. These results suggest that the increase of interpersonal body movement synchrony via interpersonal interaction can be a measurable basis of implicit social interaction. The paradigm provides a tool for identifying the behavioral and the neural correlates of implicit social interaction.