Explicit negative attitudes and blameful beliefs (e.g. poor diet, laziness) towards obese individuals are well documented and are pervasive even among health professionals. Here we sought to determine whether obesity stigma is reflected in a fundamental feature of intersubjectivity namely the automatic neural resonance with others' affective experiences. During fMRI, normal-weight female participants observed short clips depicting normal-weight (NW) and obese (Ob) models experiencing pain. Importantly, participants believed that half of the Ob were overweight due to a hormonal disorder (HormOb) and ignored the cause of obesity of the remaining models (Unknown obese models; UnkOb). Analyses of hemodynamic responses showed reduced activity to the pain of Ob compared to that of NW in areas associated with pain processing and early visual processing. The comparison between the two Ob conditions revealed a further decrease of activity to HormOb's pain compared to UnkOb's (and NW) pain in the right inferior frontal gyrus, an area associated with emotional resonance. Our study demonstrates that stigma for obese individuals can be observed at implicit levels, and that it is modulated by knowledge concerning the etiology of obesity, with the seemingly surprising result that obesity due to disease may result in greater stigmatization. Moreover, the perceived similarity with the models and the ambivalent emotion of pity may index biased brain responses to obese individuals' pain. The study highlights a possibly important neural link between resonance with the pain of others and obesity stigma.