Learners’ spatial skill is a reliable and significant predictor of achievement in STEM, including computing, education. Spatial skill is also malleable, meaning it can be improved through training. Most cognitive skill training improves performance on only a narrow set of similar tasks, but researchers have found ample evidence that spatial training can broadly improve STEM achievement. We do not yet know the cognitive mechanisms that make spatial skill training broadly transferable when other cognitive training is not, but understanding these mechanisms is important for developing training and instruction that consistently benefits learners, especially those starting with low spatial skill. This paper proposes the spatial encoding strategy (SpES) theory to explain the cognitive mechanisms connecting spatial skill and STEM achievement. To motivate SpES theory, the paper reviews research from STEM education, learning sciences, and psychology. SpES theory provides compelling post hoc explanations for the findings from this literature and aligns with neuroscience models about the functions of brain structures. The paper concludes with a plan for testing the theory’s validity and using it to inform future research and instruction. The paper focuses on implications for computing education, but the transferability of spatial skill to STEM performance makes the proposed theory relevant to many education communities.