Ischemic stroke (IS) causes various degrees of disability that sometimes induce social problems: therefore, preventing the occurrence and recurrence of IS is important. The recovery of motor function has been extensively studied. The characteristics of retrieved thrombi have become clearer; however, it is unclear what thrombi cause IS. Pulmonary vein thrombi (PVTs), such as those of the IS, can cause systemic thrombosis, by releasing several sizes of particles. PVTs are common but are underrated and can be detected via enhanced computed tomography (CT) and transesophageal echocardiography (TEE). PVTs often extend to the left atrium (LA) and can be mainly diagnosed using not enhanced CT but rather TEE. Extended LA thrombi are characterized by a lack of periodic movement with heartbeats. Direct oral anticoagulants (DOACs) are useful for preventing IS. We reported that rivaroxaban partially dissolved LA thrombi and PVTs using enhanced CT and TEE; however, the effects of edoxaban on LA thrombi and PVTs are unclear. We checked the images using enhanced CT and TEE and treated them with edoxaban. The patient was a 73-year-old female with easy fatigability. Edoxaban desirably affected the LA thrombi, and edoxaban partially dissolved the thrombi in the right lower pulmonary vein (RLPV). A decreased dose of edoxaban (15 mg, once a day) had similar effects on LA thrombi and RLPV thrombi, suggesting that this treatment could be useful for preventing IS.