The cognitive learning system is the information processing system of the brain. It takes input from the outside world and all other systems, interprets that input, and guides problem solving and decision making. Because this system is directly related to academic learning, it receives the most extensive attention from educators. The cognitive system's toughest jobs include assessing emotional sensations and social situations, then acting on those assessments to keep the primal emotions under control and the need for social belonging in perspective. In similar fashion to the emotional and social systems, the cognitive learning system relies on brain chemistry for its effectiveness.

Acetylcholine, a highly pervasive neurotransmitter, mediates synaptic activity and facilitates information processing. This neurotransmitter acts on the thalamus—a walnut-sized cluster of cell bodies serving as a relay station to sort and send sensory information to the neocortex for interpretation. Acetylcholine is ubiquitous in both its presence throughout the brain and its ability to facilitate multiple functions (e.g., attention, memory, motivation, aggression) and a host of physical behaviors (e.g., biting, clenching, chewing, facial movements, arousal, drinking, vocalization).