(1) Background: Clinical presentation, disease distribution, or treatment received may provide insights into the reasons contributing to sex differences in chronic thromboembolic pulmonary hypertension (CTEPH). (2) Methods: We evaluated 453 patients (56% women) between 2007–2019. Data was collected from REHAP (Registro Español de Hipertensión Arterial Pulmonar) registry. Two time periods were selected to evaluate the influence of new treatments over time. (3) Results: Women were older. Baseline functional class was worse, and distance walked shorter in women compared with men. Women had higher pulmonary vascular resistances. Despite this, pulmonary endarterectomy (PEA) was carried out in more men, and women received more frequently pulmonary vasodilators exclusively. The 2014–2019 interval was associated with a better survival only among women. Interestingly, women had a more distal disease during this second period of time. (4) Conclusions: Even though women were older, and received invasive treatments less frequently, mortality was similar in both sexes. The introduction of balloon pulmonary angioplasty and the improvement of pulmonary endarterectomy, especially during the last years, could be associated with a survival benefit among women.