Post pulmonary embolism (PE) dyspnea is common. Existing non-invasive studies have demonstrated that post PE dyspnea is associated with elevations in right ventricular afterload, dead space ventilation, and deconditioning. We aimed to use invasive cardiopulmonary exercise testing (iCPET) parameters in patients with post PE dyspnea to identify unique physiologic phenotypes. Are there distinct post pulmonary embolism dyspnea physiologic phenotypes described with iCPET? Patients were enrolled at the time of acute PE and through our pulmonary hypertension and dyspnea clinic. ICPET was performed if there was high suspicion for pulmonary hypertension or if there was unexplained dyspnea. A hierarchical cluster analysis was performed to identify dyspnea phenotypes. ICPET parameters assessing pulmonary hemodynamics, ventilation, and peripheral oxygen utilization were then compared within and across each cluster and with iCPET controls against peak oxygen consumption (Peak VO2). 173 patients were enrolled. Sixty-seven patients underwent iCPET. All patients had reductions in Peak VO2 and peak cardiac index relative to controls. Three clusters were identified. Cluster one was defined by having elevated RV afterload and impaired ventilatory efficiency. Cluster two had elevated RV afterload with reductions in respiratory mechanics. Cluster three had mild derangement in RV afterload with mild reductions in peak cardiac output. iCPET reveals significant heterogeneity in post PE dyspnea. Three phenotypes are characterized by differences in RV afterload, ventilatory efficiency, respiratory mechanics, and peripheral oxygen utilization.