ObjectivePulmonary embolism (PE) is a common complication of SARS-CoV-2 infection. We aimed to explore the short-term outcomes among patients with acute PE and COVID-19 and to further determine and compare the performance of the different prognostic scores (PESI, sPESI, BOVA, FAST and ESC scores) for risk-stratification in this scenario.MethodsRetrospective single-centre study of 85 patients with SARS-CoV-2 infection and PE admitted to the Emergency Department (ED). The diagnostic accuracy of each above-mentioned prognostic score was calculated post hoc, and their discriminative power was evaluated through an AUC curve.ResultsAmong the 85 patients, all-cause death occurred within 7 days for 6 patients (7.1%) and within 30 days for 14 patients (16.5%). Despite being older and having a higher percentage of altered mental status on presentation, non-survivors patients did not differ from survivors regarding comorbidities, traditional risk factors for venous thromboembolism and signs and symptoms at the ED presentation.Each risk stratification tool had modest discriminative power for 7-day mortality (AUC range, 0.601–0.730) with slightly lower discrimination for 30-day mortality (AUC range, 0.543–0.638). The pair-wise comparison of ROC curves showed that PESI had better predictive value for short-term mortality than ESC score (z test = 3.92, p = 0.001) and sPESI (z test = 2.43, p = 0.015); there is no significant difference between PESI and BOVA score (z test = 1.05, p = 0.295) and FAST score (z test = 0.986, p = 0.324).ConclusionThe most common risk-stratification tools for PE had modest discriminative power to predict short-term mortality in patients with acute PE and COVID-19.