The ‘community of inquiry’ as formulated by C. S. Peirce is grounded in the notion of communities of discipline-based inquiry engaged in the construction of knowledge. The phrase ‘transforming the classroom into a community of inquiry’ is commonly understood as a pedagogical activity with a philosophical focus to guide classroom discussion. But it has a broader application. Integral to the method of the community of inquiry is the ability of the classroom teacher to actively engage in the theories and practices of discipline-based communities of inquiry so as to become informed by the norms of the disciplines, not only to aspire to competence within the disciplines, but also to develop habits of self-correction for reconstructing those same norms when faced with novel problems and solutions, including those in the classroom. This has implications for science education and the role of educational philosophy in developing students' ability to think scientifically. But it also has broader implications for thinking critically within all key learning areas. Here we concentrate on science education. We present the parallels between philosophical inquiry and scientific inquiry that need to be realised to promote and engage with scientific inquiry in the classroom. We also discuss the conflicts between philosophical inquiry and the way inquiry science in the classroom is portrayed in the education literature. Based on philosophical and historical perceptions of science as inquiry, a practical approach to implementation of scientific inquiry in the science classroom is presented.