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Abstract We aimed to compare the effects of three intensities of treadmill running on exercise‐induced hypoalgesia (EIH) in healthy individuals. We anticipated that the primary and secondary changes in pain perception and modulation may differ between running intensities. Sixty‐six women were randomly assigned to one of three treadmill running intensities for 35 min: 40% reserved heart rate (HRR), 55% HRR, or 70% HRR. The effects of EIH were assessed using pressure pain thresholds (PPT) and tolerance thresholds (PPTol). We measured conditional pain modulation (CPM). Compared with baseline, PPT and PPTol significantly increased in all groups during running and at the 5–10‐min follow‐up. The PPT and PPTol changes in the moderate‐ and low‐intensity groups were significantly higher than those in the high‐intensity group during running and 24 h after running, while the CPM responses of the high‐intensity group were significantly reduced at the 24‐h follow‐up. Moderate‐ and low‐intensity running may elicit significant primary and secondary (persisting over 24 h) EIH effects and increase CPM responses in females. However, high‐intensity running induced only limited analgesic effects and reduced CPM responses, which may be attributed to the activation of endogenous pain modulation.