Background. Ultrasound-accelerated thrombolysis (USAT) is a safe and effective treatment for patients with intermediate–high-risk pulmonary embolism (PE). In all studies investigating USAT in the setting of PE, the recombinant tissue-plasminogen activator (rt-PA) alteplase or actilyse was used. Currently, there is a shortage of alteplase (Alteplase, Boehringer Ingelheim) in Europe. It is unknown whether the efficacy of urokinase (UK) is comparable with alteplase for USAT in patients with PE. Methods. Patients with intermediate–high-risk PE undergoing USAT with urokinase and alteplase were included in this study. One-to-one nearest neighbour matching was performed to account for baseline differences. We identified one patient treated with USAT and UK (n= 9) for each patient treated with USAT and alteplase (n= 9). Results. A total of 56 patients underwent USAT. The treatment was successful in all patients. The propensity score matched the identified nine pairs of patients. There were no statistically significant differences in the change in right ventricle-to-left ventricle (RV/LV) ratio (0.4 ± 0.3 versus 0.5 ± 0.4,p= 0.54), systolic pulmonary artery pressure (17.3 ± 8.0 versus 18.1 ± 8.1,p= 0.17), or improvement of RV function (5.8 ± 3.8 versus 5.1 ± 2.6,p= 1.0). The complication rates were comparable (11% in both groups,p= 0.55). There were no deaths in hospital or during 90 days in either group. Conclusions. In this case-matched comparison, the short-term clinical and echocardiographic outcomes showed comparable results between USAT–UK and USAT–rt-PA.