Emotion-based behaviors in humans cannot be fully explained by economic rationality. Particularly, in the ultimatum game, which incorporates conflict between self-interest and fairness, negative emotions evoked by an unfair offer seem to promote an economically irrational decision. In accordance with this suggestion, the previous studies have reported that physiological arousal is associated with rejecting unfair offers. In the present study, we investigated electrocardiogram and electrodermal activities in individuals which received fair, advantageously unfair, and disadvantageously unfair offers to specify the relations of the orienting and the defensive responses with these offers and with the decisions to accept and reject them. The results indicated that when an offer that would be rejected was presented, heart rate initially decelerated more than when an offer that would be accepted was presented. Additionally, there was a linear relationship between the deceleration and unfairness of offers. On the other hand, such different patterns were not seen in late cardiac acceleration or electrodermal response. The results suggest that because of perception of disadvantage and unpleasantness in a social context, the orienting response is evoked when an offer will be rejected. In addition, these results are discussed regarding the effect of the autonomic activity in decision-making.