Pulmonary embolism (PE) is a common disease with a considerable short- and long-term risk of death. An adequate evaluation of the prognosis in patients with PE may guide decision making in terms of the intensity of the initial treatment during the acute phase, duration of treatment, and intensity of follow-up control visits in the long term. Patients with shock or persistent hypotension are at high risk of early mortality and may benefit from immediate reperfusion. Several tools are available to define the short-term prognosis of hemodynamically stable patients. The Pulmonary Embolism Severity Index (PESI) score, simplified PESI score, and N-terminal pro-B-type natriuretic peptide levels are particularly useful for identifying patients at low risk of early complications who might be safely treated at home. However, the identification of patients who are hemodynamically stable at diagnosis but are at a high risk of early complications is more challenging. The current guidelines recommended a multiparametric prognostic algorithm based on the clinical status and comorbidities. Unfortunately, only a few studies have evaluated the role of risk factors potentially affecting the long-term prognosis of these patients. The available studies suggest a potential role of the PESI score and troponin levels evaluated at the time of an index event. However, further studies are warranted to confirm these preliminary findings and to identify other long-term prognostic factors in this setting.