Published findings from a randomized controlled trial have shown that Mindful Yoga training improves symptoms, functional deficits, and coping abilities in individuals with fibromyalgia and that these benefits are replicable and can be maintained 3 months post-treatment. The aim of this study was to collect pilot data in female fibromyalgia patients (n = 7) to determine if initial evidence indicates that Mindful Yoga also modulates the abnormal pain processing that characterizes fibromyalgia. Pre- and post-treatment data were obtained on quantitative sensory tests and measures of symptoms, functional deficits, and coping abilities. Separation test analyses indicated significant improvements in heat pain tolerance, pressure pain threshold, and heat pain after-sensations at post-treatment. Fibromyalgia symptoms and functional deficits also improved significantly, including physical tests of strength and balance, and pain coping strategies. These findings indicate that further investigation is warranted into the effect of Mindful Yoga on neurobiological pain processing.