Emotions, especially stress, affect a student’s intellectual functioning, achievement and effectiveness in problem solving. Sources of stress include new and difficult situations in which there is frustration, essentially the set of unpleasant emotions associated with the inability to implement necessities or the difficulty in solving a task or problem. The reaction to stress is often an escape from the frustrating situation or resignation, which in the case of learning leads to a reduction of effectiveness. Therefore, an important aspect of teachers’ work is helping students to relieve stress and maintain their motivation to learn. This is particularly essential for school subjects that are generally considered by students to be difficult. This article discusses the results of studies in which the eye-tracking technique was used to identify emotions, especially stress, experienced during problem solving in physics, mathematics, computer science and biology. In this experiment, eye movement parameters and survey data were analysed with the aim of obtaining information on the subjective assessment of the stress level experienced during problem solving in the field of science. Participants included 45 pupils (middle school students). The results confirm the possibility of using eye-tracking data to diagnose negative emotions. The results of the studies might also be useful for teachers, who might be able to design a system of rapid intervention and student support, with the goal of stopping students from a quick resignation of solving problems. This study fits into the new trend of neurodidactics for the development of interdisciplinary research in the area of teaching.