Objectives: This study aimed to compare the short-term and long-term follow-up outcomes of catheter-directed thrombolysis (CDT) with those of pulmonary artery embolectomy (PAE) for patients with acute pulmonary embolism (PE) included in a nationwide cohort. Background: Data allowing direct comparisons between CDT and PAE are lacking in the literature, and the optimal management of high-risk and intermediate-risk PE is still debated. Methods: A retrospective cohort study was conducted with data for 2001 through 2013 collected from the Taiwan National Health Insurance Research Database (NHIRD). Patients who were first admitted for PE and treated with either CDT or PAE were included and compared. In-hospital outcomes included in-hospital death and safety (bleeding and cardiac arrhythmias) outcomes. Follow-up outcomes included all-cause mortality and recurrent PE during the 1- and 2-year follow-up periods and through the last follow-up. Inverse probability of treatment weighting (IPTW) based on the propensity score was used to minimize possible selection bias, including indices for multimorbidity such as the Charlson’s Comorbidity Index (CCI) and HAS-BLED scores. Results: A total of 389 patients treated between January 1, 2001, and December 31, 2013, were identified; 169 underwent CDT and 220 underwent PAE. After IPTW, there were no significant differences in in-hospital mortality (18.2% vs 21.3%; odds ratio 1.07, 95% confidence interval [CI]: 0.70–1.62) or the incidence of safety outcomes between the CDT and PAE groups. The risks of all-cause mortality (30% vs 29.5%; hazard ratio 1.16, 95% CI: 0.89–1.53), recurrent PE (7.2% vs 8.7%; subdistribution hazard ratio [SHR] 0.68, 95% CI: 0.39–1.21) and new-onset pulmonary hypertension (SHR 0.25, 95% CI: 0.05–1.32) were also not significantly different between the CDT and PAE groups at 2 years of follow-up. Subgroup analysis indicated that PAE may be associated with a more favorable 2-year mortality in patients <65 years old, patients with CCI scores of <3, patients with HAS-BLED scores of 1 to 2, and patients without cardiogenic shock (all P for interaction <.05). Conclusions: In patients with PE who required reperfusion therapy, CDT and PAE resulted in similar in-hospital and long-term all-cause mortality rates and long-term rates of recurrent PE. Bleeding risks were also comparable in the 2 groups.