Pulmonary embolism (PE) is the third most frequent cardiovascular disease, characterized by a wide range of presentations and clinical courses. Prognostic assessment is a cornerstone of PE management as it determines the choice of both diagnostic and therapeutic strategies. During the previous decades significant efforts have been made to safely select patients for early discharge or home treatment, but appropriate risk stratification, particularly of intermediate-risk patients, remains challenging. In addition to the guideline-recommended clinical prediction rules, such as Pulmonary Embolism Severity Index (PESI), simplified PESI (sPESI), and/or Hestia criteria, a multimodality approach based also on biomarkers and cardiac imaging is crucial for risk-stratification and for selecting appropriate management of patients. In this review article, we discuss the current methods for predicting short and long-term prognosis in PE patients, focusing on the current guidelines, but also on the most recently proposed clinical prediction rules, biomarkers, and imaging parameters.