<p>Pre-tertiary students conducting authentic scientific research is an internationally occurring phenomenon, but it is currently poorly reported and understood in the literature. Consequently, how science teachers may best support students in their learning during authentic inquiry is functionally still opaque and not well-developed, and this paints a bleak image of in-service teachers being unimportant to the development of authentic scientist capacity. In this paper, we propose a pedagogical framework to navigate the uncertainty involved in mentoring high school students in STEM research. Five teachers from the Philippines mentoring students in authentic projects in the computational, life, and physical sciences critically investigated their empirical teaching episodes. Using the language of inferentialism, a novel interpretation we pursued as method for pedagogical reasoning, this paper proposes pragmatic steps that teachers may follow to be more intentional and explicit in their pedagogical decision-making as they navigate the uncertainties of scientific research. These findings may not only be directly helpful to “teacher scientists,” but also could scaffold future work in the teaching of STEM research to students at the secondary level and beyond.</p>