Backgroud: Personal characteristics contribute to whether negative attitudes in society are internalized as deteriorating self-stigma. Studies in healthy subjects suggest that resilience is associated with the regulation of amygdala activation by the medial prefrontal cortex (mPFC), but little is known about the factors that contribute to individual stigma resistance in psychiatric patients. Methods: We assessed stigma (by measuring association strengths between social inferiority and schizophrenia by an implicit association test) in 20 patients with schizophrenia and in 16 age- and sex-matched healthy control subjects. The brain activation strengths were measured by functional magnetic resonance imaging during evaluation of schizophrenia-related statements and of control statements. Results: Association strengths between social inferiority and schizophrenia were inversely related to the strength of the activation of the rostro-ventral mPFC. This inverse correlation survived adjustment for global functioning, depression symptom scores, and insight. Activation of the rostro-ventral mPFC was negatively correlated with activation of the amygdala. The association strengths between social inferiority and schizophrenia correlated with the compromised performance in a Stroop task, which is a measure of cognitive regulation. Discussion: Our findings suggest that individual stigma resistance is associated with emotion regulation. These findings may help to understand better stigma resistance and thereby aid the development of patient interventions that add to the public anti-stigma work in reducing devastating effects of stigma.