Background Acute pulmonary embolism (PE) remains a leading cause of cardiovascular morbidity and mortality, particularly in emergency settings where rapid clinical decisions are critical. This study aimed to compare the clinical characteristics, management strategies, and short-term outcomes of patients diagnosed with acute PE in the emergency department. Methods This observational comparative study was conducted at the Emergency Department of Ayub Medical College and its teaching hospital, from January 2022 to January 2023. A total of 89 patients with confirmed acute PE were enrolled. Data were analysed using SPSS version 26.0. Continuous variables were compared using the independent t-test or Mann–Whitney U test, while categorical variables were analyzed using the Chi-square or Fisher’s Exact Test. A p value < 0.05 was considered statistically significant. Results The mean age of patients was 56.7 ± 14.2 years, with a slight male predominance (57.3%). While no significant association was found between demographic variables and in-hospital mortality (p > 0.05), several clinical and radiological factors showed strong correlations with adverse outcomes. Patients who died had significantly higher respiratory rates (p = 0.031), lower oxygen saturation (p = 0.019), and more frequent RV dysfunction on echocardiography (p = 0.041). Central thrombi in the main pulmonary artery were significantly associated with higher mortality (p = 0.0012). ICU admission also showed a strong association with death (p = 0.0073), while thrombolysis was significantly linked with shorter hospital stays (p = 0.0165). The overall in-hospital mortality rate was 7.9%, and the 30-day mortality was 10.1%. Conclusion This study highlights the prognostic importance of thrombus location, respiratory compromise, and right heart strain in acute PE. Early identification of high-risk features and tailored management strategies, including timely thrombolysis and ICU monitoring, can significantly improve patient outcomes in emergency settings.