Modern neuroscientific research has substantially enhanced our understanding of the human brain. However, many challenges remain in developing a strong, brain-based theory of human learning, especially in complex environments such as educational settings. Some of the current issues and challenges in our progress toward developing comprehensive neuroscientific-based theories of human learning, particularly in the academic disciplines, are reviewed, beginning with a brief summary of the history of publications in science learning. This is followed by an analysis of some of the large-scale issues and conceptual problems that we currently face in developing a strong, middle-ground "neuroeducational theory" relevant to learning, especially in rather abstract disciplines such as mathematics and science. Finally, some perspectives on possible future strategies and challenges in reaching the goal of a neuroeducational theory are presented.