People engaged in interactive decision making rely on prior decision behaviors by other persons to make new choices and they exhibit inter-brain synchrony between each other. The functional meanings of such inter-brain synchrony, however, remains obscure. In the present study, dyads (15 pairs, all female) played the Prisoner's Dilemma game while their brain activities were recorded simultaneously by electroencephalography (EEG)-based hyperscanning technique. We manipulated the context of the game with higher versus lower cooperation index (HCI vs. LCI) and to each participant, we depicted the interaction as involving either another human partner or a machine (H-H vs. H-M). The results showed a higher cooperation rate and larger theta/alpha-band inter-brain synchrony in condition H-H than in H-M. In the condition H-H, there were larger centrofrontal theta-band and centroparietal alpha-band inter-brain synchrony in tasks set for high cooperation (HCI vs. LCI). Enhanced inter-brain synchrony covaried with increased cooperative choices observed between LCI and HCI. Furthermore, a subjective measure of perceived cooperativeness mediated the relationship between game context and inter-brain synchrony. These findings provide evidence for a role of cooperation on inter-brain synchrony during interactive decision making, and suggest distinct underlying neural processes recruited by cooperation contexts to enable high-level social cognitive processing in decision making.