The presence of artificial agents in our everyday lives is continuously increasing. Hence, the question of how human social cognition mechanisms are activated in interactions with artificial agents, such as humanoid robots, is frequently being asked. One interesting question is whether humans perceive humanoid robots as mere artifacts (interpreting their behavior with reference to their function, thereby adopting the design stance) or as intentional agents (interpreting their behavior with reference to mental states, thereby adopting the intentional stance). Due to their humanlike appearance, humanoid robots might be capable of evoking the intentional stance. On the other hand, the knowledge that humanoid robots are only artifacts should call for adopting the design stance. Thus, observing a humanoid robot might evoke a cognitive conflict between the natural tendency of adopting the intentional stance and the knowledge about the actual nature of robots, which should elicit the design stance. In the present study, we investigated the cognitive conflict hypothesis by measuring participants’ pupil dilation during the completion of the InStance Test. Prior to each pupillary recording, participants were instructed to observe the humanoid robot iCub behaving in two different ways (either machine-like or humanlike behavior). Results showed that pupil dilation and response time patterns were predictive of individual biases in the adoption of the intentional or design stance in the IST. These results may suggest individual differences in mental effort and cognitive flexibility in reading and interpreting the behavior of an artificial agent.