Rapid development of neuroimaging techniques in recent decades has raised a wave of new insights about emotion, motivation, learning, development and thinking. In the light of these new insights, educators can derive effective implications and principles for improving educational policies and practices based on biological foundation of learning and thinking. In this paper is concentrated on some of those effective implications for improving students' conceptual thinking as a primary function of the cerebral cortex and a recognized form of thinking that includes aspects of critical, creative, and metacognitive thinking. This paper is introducing a framework for improving students' conceptual thinking based on how learning and thinking occur in the brain. Literature review revealed that designing instruction based on concepts, projects, problems, and themes are the most important brain compatible instruction design models in improving conceptual thinking
