Many students encounter difficulties in science and mathematics that may stem from intuitive interference of salient irrelevant variables. We focused on the comparison of perimeters task, in which area is the irrelevant salient variable. In congruent trials (no interference), accuracy is higher and reaction time is shorter than in incongruent trials (area variable interference). A brain-imaging study related to this task indicated that correctly answering the incongruent condition is associated with activation in prefrontal brain regions known for their executive inhibitory control. In the current study we explored the relationship between inhibitory control mechanisms and the ability to overcome intuitive interference. Participants in the study were 90 ninth graders. The efficiency of their inhibitory control mechanisms was assessed and accuracy and reaction time of correct responses in the comparison of perimeters task were recorded. The findings indicate that students with efficient inhibitory control mechanisms scored significantly better in the incongruent conditions than did those with inefficient ones. In addition, the findings indicate that the higher the efficiency of inhibitory control mechanisms, the better students were in overcoming the intuitive interference. These findings indicate the importance of inhibitory control mechanisms in overcoming interference in science and mathematics. They point to the possibility of improving students’ ability to overcome intuitive interference by strengthening their inhibitory control mechanisms. We also demonstrate that applying cognitive psychology and neuroscience methodologies in science and mathematics education research contributes to both fields.