Venous thromboembolism, in particular, pulmonary embolism (PE), is a significant contributor to the morbidity and mortality associated with COVID-19. In this study, we utilized the National Inpatient Sample (NIS) database 2020 to evaluate and compare clinical outcomes in patients with COVID-19 with and without PE. Our sample includes 1,659,040 patients hospitalized with COVID-19 pneumonia between January 2020 and December 2020. We performed propensity-matched analysis for patient characteristics and in-hospital outcomes, including the patient’s age, race, sex, insurance status, median income, length of stay, mortality, hospitalization cost, comorbidities, mechanical ventilation, and vasopressor support. Patients with COVID-19 with PE had a higher need for mechanical ventilation (25.7% vs. 15.6%, adjusted odds ratio 1.4, 95% CI 1.4–1.5, p p p p < 0.001). This study highlights the need for more aggressive management of PE in COVID-19-positive patients with the aim to improve early diagnosis and treatment to reduce morbidity, mortality, and healthcare costs seen in the synchronous COVID-19 and PE-positive patients.