Advances in brain imaging have led to a paradigm shift in neuroscience research, moving from focusing on individual brain structures to investigating neural networks and connections. However, neuroanatomy education still tends to concentrate on discrete brain regions. Two separate experiments in undergraduate neuroscience courses investigated whether incorporating neural connectivity into neuroanatomy education would enhance learning. Students in each experiment learned to identify brain structures through computer-based training sessions that provided text-based narrative feedback about neural connections, followed by final memory tests after a 1-month delay. The first experiment included 30 students and demonstrated a long-term memory benefit associated with described neural connections, showing a medium effect size (p = 0.01, d = 0.54) comparable to the established retrieval practice effect for enhancing long-term memory (p = 0.03, d = 0.47). The second experiment replicated the benefits of described neural connections with a small effect size (p = 0.005, d = 0.28) in a larger sample of 122 students across classrooms at two universities. Furthermore, students remembered the functional outcomes of neural connections from training (p < 0.001, d = 0.46), and this generalized to clinical applications (p = 0.009, d = 0.27). In contrast, categorizing brain areas without describing neural connections (as is commonly done in introductory neuroscience textbook chapters) did not benefit either memory or generalization. Findings demonstrate that leveraging the connectivity paradigm shift in neuroscience research can enhance neuroanatomy education. Emphasizing neural connections and their functional outcomes helps simplify neuroanatomy and improve understanding and retention.