Herein, we assess the use of the Acute Physiology and Chronic Health Evaluation-IV (APACHE-IV) and pulmonary embolism (PE)-specific risk scores to predict mortality among intensive care unit (ICU) patients who developed secondary PE. This retrospective cohort study used information from 208 United States critical care units recorded in the eICU Collaborative Research Database during 2014 and 2015. We calculated APACHE-IV, Pulmonary Embolism Severity Index (PESI), simplified PESI (sPESI), and ICU-sPESI scores and compared their predicting performance using the area under the receiver operating characteristic (AUROC) curve. Of 812 patients included in our study, 150 died (mortality, 18.5% [95% CI, 15.8%-21.1%]). Compared to survivors, non-survivors had higher APACHE-IV (86 vs 52, P<0.001), PESI (170 vs 129, P<0.001), sPESI (2 vs 2, P<0.001), and ICU-sPESI (4 vs 2, P<0.001) scores. AUROCs were 0.790 (APACHE-IV); 0.737 (PESI); 0.726 (ICU-sPESI); and 0.620 (sPESI). APACHE-IV performed significantly better than all 3 PE-specific mortality scores (APACHE-IV vs PESI, P=0.041; APACHE-IV vs sPESI, P=0.001; and APACHE-IV vs ICU-sPESI, P=0.021). Both the PESI and ICU-sPESI outperformed the sPESI (PESI vs sPESI, P=0.001; ICU-sPESI vs sPESI, P<0.001). APACHE-IV score was found to be the best instrument for predicting mortality risk, but PESI and ICU-sPESI scores may be used when APACHE-IV is unavailable. sPESI AUROC suggests absence of sufficient discriminative value to be used as a predictor of mortality in patients with secondary PE.