Early STEM education is crucial for later learning. This novel study utilised fNIRS to examine how STEM teaching methods (i.e., traditional, storytelling, storyboarding) affect neural activity synchronisation between teachers and students. Our results showed that left and right inferior frontal gyrus (IFG) for storytelling teaching versus traditional teaching, superior temporal gyrus for storyboard teaching versus traditional teaching, and left angular gyrus for storyboard and storytelling teaching were significant different in brain synchronisation. In the storytelling teaching condition, left supramarginal gyrus brain synchrony was found to improve STEM learning outcomes. In the storyboard teaching condition, IFG brain synchrony correlated positively with STEM learning improvement. The findings confirmed that story-based teaching and storyboarding can improve STEM learning efficacy at the neural level and unscored the significant role of neural synchronization as a predictor of learning outcomes.