Little is known of the effects of flexibility stigma on employee outcomes. Flexibility stigma refers to the negative sanctions received by those who seek flexible work practices to manage work and family requirements. Using stigma theory, this study investigates the effect of flexibility stigma on employee well‐being and turnover intentions. Drawing on ecological systems theory, it also investigates the effect of flexibility stigma on flexible work practices usage. Further, integrating the above‐mentioned two theories, this study predicts the mediating role of flexible work practices usage in the flexibility stigma–employee outcomes relationship. Using survey data from 293 employees of an Australian organisation, we found that stigma has a negative effect on employee well‐being, a positive effect on turnover intentions, and a negative effect on flexible work practices usage. We also found pioneering evidence for the proposed partial mediation effect. Theoretical, research and practical contributions are discussed.