The experience of fear is closely linked to the survival of species. Fear can be conceptualized as a brain state that orchestrates defense reactions to threats. To avoid harm, an organism must be equipped with neural circuits that allow learning, detecting, and rapidly responding to threats. Past experience with threat can transform neutral stimuli present at the time of experience into learned threat‐related stimuli via associative learning. Pavlovian threat conditioning is the central experimental paradigm to study associative learning. Once learned, these stimulus–response associations are not always expressed depending on context or new experiences with the conditioned stimuli. Neural circuits mediating threat learning have the inherent plasticity to adapt to changing environmental threats. Encounters devoid of danger pave the way for extinction or reconsolidation to occur. Extinction and reconsolidation can both lead to changes in the expression of threat‐induced defense responses, but differ in stability and have a different neural basis. This review presents the behavioral models and the system‐level neural mechanisms in animals and humans of threat learning and modulation. WIREs Cogn Sci 2015, 6:427–439. doi: 10.1002/wcs.1353This article is categorized under: Psychology > Emotion and Motivation Psychology > Memory Psychology > Theory and Methods