Novel Coronavirus disease (COVID-19) has been widely described as the cause for a proinflammatory and hypercoagulable state. The inflammatory process involving the alveolar vascular endothelium in the respiratory system, is a determining factor for the onset of primary Pulmonary Artery Thrombosis (PAT) even in patients with heparin prophylactic treatment. Little is known about the efficacy of the anticoagulant therapy during the course of PAT caused by COVID-19. In this paper we describe the results obtained in patients with moderate COVID-19 disease, previously threated with prophylactic enoxaparin, who then received full Anticoagulant treatment after diagnosis of PAT. After three months Computed Tomography Pulmonary Angiography demonstrated a complete resolution of the vascular obstructive lesions in all patients, while all the coagulation tests were normal.