A 23-year-old man presented with a fever, shaking chills, headaches, nausea, and a dry cough. Investigations showed lymphocytic leukocytosis with atypical lymphocytes in a blood smear. Liver function test results, D-dimer concentrations, and fibrin degradation product concentrations were greatly elevated. Computed tomography of the whole body with contrast showed hepatosplenomegaly with splenic infarction and bilateral pulmonary embolism without deep vein thrombosis. Cytomegalovirus (CMV) immunoglobulin M, and serum CMV pp65 antigenemia were positive, and serum () antibody was also highly positive. These results suggested the diagnosis of co-infection of CMV and complicated by systemic arteriovenous thrombosis, which resulted in pulmonary embolism and splenic infarction. After he started edoxaban tosilate hydrate for the thrombosis, his symptoms resolved in a few days. To the best of our knowledge, this is the first case of co-infection of CMV and leading to pulmonary embolism and splenic infarction.