A retrospective analysis from the Saudi Arabian Pulmonary Hypertension Registry (2011–2022) included 37 patients with CTEPH associated with antiphospholipid syndrome (APS) and 41 patients without APS who underwent pulmonary endarterectomy (PEA). Persistent pulmonary hypertension (PH) occurred in 43% of patients with no significant difference between groups. Patients with APS-CTEPH who received pulmonary vasodilator therapy before surgery had a lower risk of persistent PH. Postoperative complications were significantly more frequent in the group with APS (p=0.002). The group with APS had a higher incidence of rehospitalization during the first year after surgery. Despite these risks, the 5-year survival rate was 98.3% with no difference between groups. APS does not increase the risk of persistent PH or affect long-term mortality in this cohort.