EMDR is based on the understanding that all humans have a physiologically-based information processing system. This information processing system processes the multiple elements of our experiences (such as sensations, emotions, words, and other types of input) and stores memories in an accessible and useful form. Memories are linked in networks that contain related thoughts, images, emotions, and sensations. Learning occurs when new associations are forged with material already stored in memory.

When a traumatic or very negative event occurs, information processing may be incomplete, perhaps because strong negative feelings or dissociation interfere with information processing. The memory is then dysfunctionally stored without appropriate associative connections and with many elements still unprocessed. When the individual thinks about the trauma, or when the memory is triggered by similar situations, the person may feel like she is reliving it, or may experience strong emotions and physical sensations. A prime example is the intrusive thoughts, emotional disturbance, and negative self-referencing beliefs of posttraumatic stress disorder (PTSD). Information processing is thought to occur when the targeted memory is linked with other more adaptive information. Learning then takes place, and the experience is stored with appropriate emotions, able to appropriately guide the person in the future.