Background: In this study, we aimed to compare echocardiography, electrocardiography (ECG) abnormalities, Doppler ultrasonography (USG), and computed tomography pulmonary angiography (CTPA) results in predicting acute pulmonary embolism (PE) patients’ 3-month mortality. Methods: This retrospective cohort study included 124 patients (72 females, 52 males) with acute PE. Demographics, symptoms, clinical signs, comorbidities, history of surgery, arterial blood gas, liver-renal functions, complete blood count, echocardiography, ECG, Doppler USG, and CTPA results, as well as 3-month mortality were recorded. Results: pH (z = –2.623; p <0.01), hemoglobin (z = –3.112; p <0.01), and oxygen saturation (z = –2.165; p <0.01) were significantly higher in survivors. White blood cell (z = –2.703; p <0.01), blood urea nitrogen (z = –3.840; p <0.01), creatinine (z = –3.200; p <0.01), respiratory rate (z = –2.759; p <0.01), and heart rate (z = –2.313; p <0.01) were significantly higher in non-survivors. Nonspecific ST changes (AUC 0.52, 95% CI 0.43–0.61), p pulmonale (AUC 0.52, 95% CI 0.43–0.61), normal axis (AUC 0.61), right axis deviation (AUC 0.56), right ventricle strain pattern (AUC 0.59), and right pulmonary artery embolism (AUC 0.54) on CTPA showed the highest mortality prediction. Conclusions: Nonspecific ST changes, p pulmonale, normal axis and right axis deviation in ECG, RV strain in echocardiography, and right pulmonary artery embolism on CTPA are associated with a higher mortality.