Background We have previously reported important strain differences in response to SU5416 (SU, a vascular endothelial growth factor receptor 2 inhibitor) in rats and have identified a specific colony of Sprague‐Dawley rats that are hyperresponsive (SD ^HR ) to SU alone and develop severe pulmonary arterial hypertension (PAH) with a single injection of SU, even in the absence of hypoxia. Interestingly, SD ^HR rats exhibit incomplete penetrance of the severe PAH phenotype with an “all‐or‐none” response to SU alone, which provides a unique opportunity to assess the influence of female sex and sex hormones on susceptibility to PAH after endothelial injury in a genetically prone model. Methods and Results SD ^HR rats were injected with SU (20 mg/kg SC) and, in the absence of hypoxia, 72% of male but only 27% of female rats developed severe PAH at 7 weeks, which was associated with persistent endothelial cell apoptosis. This sex difference in susceptibility for severe PAH was abolished by ovariectomy. Estradiol replacement, beginning 2 days before SU (prevention), inhibited lung endothelial cell apoptosis and completely abrogated severe PAH phenotype in both male and ovariectomized female rats, while progesterone was only protective in ovariectomized female rats. In contrast, delayed treatment of SD ^HR rats with established PAH with estradiol or progesterone (initiated at 4 weeks post‐SU) failed to reduce lung endothelial cell apoptosis or improve PAH phenotype. Conclusions Female sex hormones markedly reduced susceptibility for the severe PAH phenotype in response to SU alone in a hyperresponsive rat strain by abolishing SU‐induced endothelial cell apoptosis, but did not reverse severe PAH in established disease.