This article investigates the differences in cognitive and neural mechanisms between human-human and human-virtual agent interaction using a dataset recorded in an ecologically realistic environment. We use Convergent Cross Mapping (CCM) to investigate functional connectivity between pairs of regions involved in the framework of social cognitive neuroscience, namely the fusiform gyrus, superior temporal sulcus (STS), temporoparietal junction (TPJ), and the dorsolateral prefrontal cortex (DLPFC)—taken as prefrontal asymmetry. Our approach is a compromise between investigating local activation in specific regions and investigating connectivity networks that may form part of larger networks. In addition to concording with previous studies, our results suggest that the right TPJ is one of the most reliable areas for assessing processes occurring during human-virtual agent interactions, both in a static and dynamic sense.