In this chapter, we bridge research on scientific and counterfactual reasoning. We review findings that children struggle with many aspects of scientific experimentation in the absence of formal instruction, but show sophistication in the ability to reason about counterfactual possibilities. We connect these two sets of findings by reviewing relevant theories on the relation between causal, scientific, and counterfactual reasoning before describing a growing body of work that indicates that prompting children to consider counterfactual alternatives can scaffold both the scientific inquiry process (hypothesis-testing and evidence evaluation) and science concept learning. This work suggests that counterfactual thought experiments are a promising pedagogical tool. We end by discussing several open questions for future research.