Background: The prevalence of anticoagulant therapy-associated hemorrhagic complications in hospitalized patients with pulmonary embolism (PE) has been scarcely investigated. Aim: To evaluate the prevalence of hemorrhages in hospitalized PE patients. Methods: The Information System “ASKLIPIOS™ HOSPITAL” implemented in the Respiratory Medicine Department, University of Thessaly, was used to collect demographic, clinical and outcome data from January 2013 to April 2021. Results: 326 patients were included. Males outnumbered females. The population’s mean age was 68.7 ± 17.0 years. The majority received low molecular weight heparin (LMWH). Only 5% received direct oral anticoagulants. 15% of the population were complicated with hemorrhage, of whom 18.4% experienced a major event. Major hemorrhages were fewer than minor (29.8% vs. 70.2%, p = 0.001). Nadroparin related to 83.3% of the major events. Hematuria was the most common hemorrhagic event. 22% of patients with major events received a transfusion, and 11% were admitted to intensive care unit (ICU). The events lasted for 3 ± 2 days. No death was recorded. Conclusions: 1/5 of the patients hospitalized for PE complicated with hemorrhage without a fatal outcome. The hemorrhages were mainly minor and lasted for 3 ± 2 days. Among LMWHs, nadroparin was related to a higher percentage of hemorrhages.