Abstract Background People living with severe obesity report high levels of weight-related stigma. Theoretically, this stigma undermines weight loss efforts. The objective of this study is to test one proposed mechanism to explain why weight loss is so difficult once an individual becomes obese: that weight-related stigma inhibits physical activity via demotivation to exercise. Methods The study focused on individuals who had bariatric surgery within the past 5 years (N = 298) and who report a post-surgical body mass index (BMI) ranging from 16 to 70. Exercise avoidance motivation (EAM) and physical activity (PA) were modeled as latent variables using structural equation modeling. Two measures of weight stigma, the Stigmatizing Situations Inventory (SSI) and the Weight Bias Internalization Scale (WBIS) were modified for people with a long history of extreme obesity for use as observed predictors. Results Exercise avoidance motivation (EAM) significantly mediated the association between both experienced (SSI) and internalized (WBIS) weight stigma and physical activity (PA) in this population. Conclusion Exercise avoidance motivation, influenced by weight stigma, may be a significant factor explaining the positive relationship between higher body weights with lower levels of physical activity.