Contemporary research into science education has generally been conducted from the perspective of "conceptual change" in learning. This study sought to extend previous work by recognizing that human rationality can be influenced by the emotions generated by the learning environment and specific actions related to learning. Methods used in educational psychology were adopted to investigate the emotional experience of science students as affected by gender, teaching methods, feedback, and learning tasks. A multidisciplinary research approach combining brain activation measurement with multivariate psychological data theory was employed in the development of a questionnaire intended to reveal the academic emotions of university students in three situations: attending science class, learning scientific subjects, and problem solving. The reliability and validity of the scale was evaluated using exploratory and confirmatory factor analyses. Results revealed differences between the genders in positive-activating and positive-deactivating academic emotions in all three situations; however, these differences manifested primarily during preparation for Science tests. In addition, the emotions experienced by male students were more intense than those of female students. Finally, the negative-deactivating emotions associated with participation in Science tests were more intense than those experienced by simply studying science. This study provides a valuable tool with which to evaluate the emotional response of students to a range of educational situations.