The theoretical basis for the Energy in the Human Body Curriculum lies in constructivism and model based teaching and learning theory. Many researchers in science education now believe that students must actively construct knowledge rather than receive it passively from teachers or textbooks. Instead of being "blank slates" upon which facts and theories are inscribed, students have many ideas about how the world works even before any formal instruction takes place. However, often times the theories and models they construct differ from the scientifically accepted model. Effective teaching and learning, therefore, occurs when teachers attempt to discover students' pre-existing ideas at the start of instruction, then use these ideas to help students confirm or modify the model as appropriate. Students' ideas about a topic are described as "mental models." These mental models include preconceptions, alternative conceptions, and naïve conceptions that are stored as representations or mental images to explain the world around them. The process of learning is the gradual modification of these models held by students before instruction in response to questions and other stimuli supplied by teachers, other learners, or the students themselves.

Constructivism is an educational theory that views learning as an active process in which learners construct knowledge. This process involves using past knowledge or ideas, patterns or schemas in the mind, and new experiences. Constructivism differs from approaches to teaching that see learners as passive receivers of knowledge. More recently researchers have realized that the learning process is not only the result of the learner cognitive ability but it is also the result of the interaction with peers and teachers. This new idea of conceiving learning in which participate individual as well as social processes is called social constructivism.

Model-Based Reasoning Theories are in opposition to the rules of formal reasoning theories and deal with mental models of systems (biological or conceptual) that individuals use to think about the behavior of the systems. The world around us is complex and dynamic, but we cannot know or apprehend it directly. As a result, subjects, including students and scientists, build dynamic and evolving explanations or mental models to make sense of that reality. In other words, (If we accept the idea that in order to learn effectively, we must think about what we are learning, then we must simplify the world in order to think about it.) when we think about a problem or a situation, we somehow represent it in our mind. This representation is a mental model. In most people, this representation is primarily visual, although people may use words to augment their thinking or their explanation to others. When individuals use the model to reason, , they are able to run and manipulate this mental model to give explanations for phenomena, to try out new ideas, and to test for the applicability of the model to new situations. However, mental models are not finished representations but are naturally evolving mental schema (or may produce several intermediate models) that often may still contain incomplete, unstable, and unscientific information.

The area of science and research that deals with how people reason using these mental models is know as Model Based Teaching and Learning Theory (MBTL). This theory takes into consideration the importance of mental models that students bring to the learning situation. It recognized that students have developed these models to help them explain the world around them and that they are not readily displaced or built simply because they are given or shown another mental model that may belong to scientists, the teacher, or textbook. To help students in the difficult process of modifying their mental models, the teacher first must recognize the student's mental model and then choose strategies to cause the student to be dissatisfied enough to want to change.

Educators often find that students have strongly-held ideas that are different from ones that have been developed in modern science. These ideas are often called misconceptions, alternative conceptions, preconceptions or naïve conceptions. In this curriculum 'Preconception' refers to a conception held prior to instruction in a particular topic. It is the mental model a student brings to the particular learning experience. 'Alternative conception' (sometimes called a misconception) refers to those conceptions that are incompatible with currently accepted scientific conceptions. 'Naïve conception' refers to those conceptions students hold that, while not incompatible with currently accepted theory, are simplistic conceptions that are not scientifically complete from an expert's view. We will use the term 'Prior model' to refer to either an alternative conception (misconception), naïve conception, or an intermediate model, as developed during instruction, that the student brings to the learning situation. Sometimes these preconceptions are held quite strongly, and students may return to them even after instruction. Countering misconceptions often requires helping them understand why their idea may not be useful when explaining new phenomena. On the other hand, telling them it is wrong rarely proves effective.