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Recent research on motivation to learn science shows that science teaching usually supports students’ systemising, but not their empathising cognition. In this paper we argue that empathy, with due caution, should be emphasised in science learning more seriously and consistently, particularly in a Science|Environment|Health pedagogy that aims at fostering the mutual benefit between the three interlinked educational fields. After briefly recapitulating research results about the empathising-systemising (E-S) theory and motivation to learn science, the paper describes the science of empathy and then reflects on the opportunities and challenges of introducing empathy into science teaching. Many studies of effective science learning can be found that involve empathising, though this usually is not made explicit. Thus, bringing empathy into play sheds another light on successful science learning and helps in unfolding its full potential. Moreover, considerations about the role of values in science education entail the insight that, when it comes to complex socio-scientific issues, including empathy is not only useful, but actually vital. The concept of reflective equilibrium, taken from applied ethics, provides a framework for the consideration of both systematic and empathic aspects in science teaching. This undervalued approach promises to involve all students and is therefore a genuine science for all approach.