This clinical trial investigated the effect of an Emotional Freedom Techniques (EFT) intervention on brain activation in chronic pain sufferers using functional magnetic resonance imaging (fMRI). EFT is a brief stress reduction technique which combines stating a cognitive statement with somatic tapping on acupressure points. Twenty-four adults were allocated to a six-week online group EFT treatment and underwent resting-state fMRI pre and post the intervention. A repeated measures MANOVA indicated significant differences in the levels of pain severity (−21%), pain interference (−26%), quality of life (+7%), somatic symptoms (−28%), depression (−13.5%), anxiety (−37.1%), happiness (+17%), and satisfaction with life (+8.8%) from pre-to post-test. Cohen's effect sizes ranged from small (0.2) to large (0.75) values suggesting significance for the intervention. fMRI analysis showed post-EFT treatment significantly decreased connectivity between the medial prefrontal cortex (a pain modulating area) and bilateral grey matter areas in the posterior cingulate cortex and thalamus, both areas being related to modulating and catastrophizing of pain. There were no brain areas that showed significantly increased connectivity post-EFT treatment. Coupled with the psychological measures the findings support the effects of the EFT intervention in reducing chronic pain and its impacts. Recommendations for future research are discussed.