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In this single-case MEG pilot study, an Emotional Freedom Technique (EFT) intervention produced regulation of brain regions exhibiting treatment effects in response to conventional psychotherapy and medication. The neural correlates of the threat response were attenuated, and heightened activation of brain frontal executive regions mediating limbic responses appraisal to stressful stimuli was recorded. These pilot results are consistent with the literature indicating that EFT is an evidence-based treatment for phobias. They provide for the first time knowledge regarding the neurophysiological mechanisms underlying the treatment effects. This study pioneers the methodology required to conduct randomized controlled trials.