Event-related potentials are used to test the hypothesis that an intuitive misconception persists in the mind even after the acquisition of scientific knowledge. We investigated the temporal dynamics of neural mechanisms in solving a scientific problem involving a common misconception. It showed that the increased P2 component was elicited by the stimulus congruent with the misconception. The increased N2 component was elicited by the stimulus incongruent with the misconception. Additionally, the enhanced late positive potential component was evoked by the stimulus involving the conflict between the misconception and scientific knowledge. These results suggest that an intuitive misconception might still survive after the acquisition of scientific knowledge. It could be invoked automatically to evaluate the plausibility of incoming information. Subsequently, scientific knowledge is explicitly retrieved to monitor the conflict and inhibit the misconception. This study might have values in revealing the neural correlates of knowledge representation and scientific reasoning in education.