While being exposed to an intensive tonic pain stimulus at one area of the body, another phasic pain stimulus applied to a remote site is perceived as less painful. The neurophysiological basis for this "pain inhibits pain" phenomenon has been presumed to be an activation of the spino-bulbo-spinal mechanism termed "diffuse noxious inhibitory controls." However, several additional mechanisms such as an activation of the descending pain control system may contribute to this observation. Here we investigated the underlying supraspinal mechanisms of "heterotopic noxious conditioning stimulations" (HNCS), representing this specific experimental constellation. We used functional magnetic resonance imaging and behavioral recordings in combination with a modified cold-pressor task and phasic painful stimuli, and investigated the contribution of endogenous opioids to this mechanism using the opioid antagonist naloxone in a double-blind crossover design. HNCS led to marked endogenous analgesia and this effect correlated positively with the perceived intensity of the tonic painful stimulus. Furthermore, HNCS was paralleled by reduced blood oxygen level dependent (BOLD) responses in classical pain-responsive regions. Conversely, HNCS led to tonic BOLD increases in subregions of the anterior cingulate cortex. The strength of functional coupling between the subgenual anterior cingulate cortex and key structures of the descending pain control system was enhanced during HNCS, which correlated positively with the individual endogenous analgesia during HNCS. These effects were in part reversed by naloxone, speaking for the contribution of endogenous opioid neurotransmission to this mechanism. Taken together, these results demonstrate a substantial contribution of higher-order brain regions to the phenomenon of hypoalgesia during HNCS. Functional magnetic resonance imaging shows how the human brain is involved in heterotopic noxious conditioning and reveals active supraspinal pain modulatory mechanisms during dual pain stimulation.