Bone marrow edema syndrome (BMES) refers to clinical condition describing an area of low signal density on T1-weighted MRI, and could result from infection, inflammation, neoplasm, injury, and osteoarthritis. Rarely, BMES could occur in 13 % of the patient with primary anti-phospholipid syndrome (APS), and its association with early avascular necrosis (AVN) was well-known. Here, we describe a case of 67-year-old male with a history of previous transient ischemic attack (TIA), who presented with fever of unknown origin (FUO) and both knee pain. We did serologic test including autoimmune marker to work up FUO. Both IgG and IgM aCL were detected in high titer (> 150 GPL and >150 MPL, respectively), and its positivity was remained after 3 months. So, primary APS was diagnosed according to Sapporo criteria. We performed MRI to evaluate knee pain, and MR images showed diffuse bone marrow edema with enhancement after administration of gadolinium in both knee joints. Finally, he was diagnosed as having a BMES which was considered as a thrombotic complication in the context of APS. We administered intravenous heparin and switched to warfarin after 1 week. His symptoms of both knee arthralgia had been improved after the introduction of NSAIDs (non-steroidal anti-inflammatory drugs) and anticoagulation medication. Recently, we performed follow-up MRI and that showed improvement of bone marrow edema lesions. Our case suggests that BMES can be developed in a patient of APS, suggesting that early diagnosis and treatment in the stage of BMES could prevent AVN, inevitable devastating complication of primary APS.