One agenda of science instruction in primary schools is to develop learners' scientific reasoning abilities and to equip them with the necessary twenty-first-century skills. Few studies have been conducted to develop measurement tools that aspire to assess primary school learners' scientific reasoning. Most of these studies lack a theoretical model backing the development of these assessment tools. This paper introduces the model for measuring scientific reasoning (MMSR) as a theoretical model for guiding the development of assessment tools in the context of measuring upper primary school learners' scientific reasoning. We first conceptualise scientific reasoning using a review of the literature and then present evidence to justify and validate this model for use in measuring primary school learners' scientific reasoning abilities. Furthermore, using research in history and philosophy of science and science education, the MMSR model supports the development of assessment tools measuring learners' patterns of scientific reasoning and also considering the nature of science across different contextual settings.