Acute pulmonary embolism (PE) is not only a serious and potentially life-threatening disease in the acute phase, in recent years it has become evident that it may also have a major impact on a patient’s daily life in the long run. Persistent dyspnea and impaired functional status are common, occurring in up to 50% of PE survivors, and have been termed the post-PE syndrome (PPES). Chronic thromboembolic pulmonary hypertension is the most feared cause of post-PE dyspnea. When pulmonary hypertension is ruled out, cardiopulmonary exercise testing can play a central role in investigating the potential causes of persistent symptoms, including chronic thromboembolic pulmonary disease or other cardiopulmonary conditions. Alternatively, it is important to realize that post-PE cardiac impairment or post-PE functional limitations, including deconditioning, are present in a large proportion of patients. Health-related quality of life is strongly influenced by PPES, which emphasizes the importance of persistent limitations after an episode of acute PE. In this review, physiological determinants and the diagnostic management of persistent dyspnea after acute PE are elucidated.