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Chronic post-stroke headache is a common yet understudied complication of stroke, potentially driven by maladaptive connectivity between limbic and sensorimotor brain regions. This pilot study evaluated the effects of a combined intervention using repetitive transcranial magnetic stimulation (rTMS) and moderate-intensity exercise on resting-state functional connectivity and self-reported pain outcomes in individuals with persistent post-stroke headache. Five participants completed ten sessions of rTMS targeted to the primary motor cortex followed by aerobic exercise within a 2-hour window. Resting-state fMRI and behavioral data were collected at baseline and post-intervention. Seed-based analyses revealed reduced connectivity between the amygdala, insula, and thalamus and regions involved in salience, sensory, and cognitive control. Self-reported pain severity and interference also showed mean reductions over the course of the study. These findings support the feasibility and potential neural and behavioral impact of combined neuro-modulatory and behavioral interventions for managing chronic pain after stroke.