A 37-year-old woman with extranodal marginal-zone lymphoma was admitted with a fever, hemiplegia, and severe dyspnea after chemotherapy. Catastrophic antiphospholipid antibody syndrome (CAPS) was suspected based on the histopathological confirmation of small-pulmonary vessel occlusion, evidence of the involvement of three organs, and elevated lupus anticoagulant assay results in a short time span. The patient responded to the initial treatment. One month later, the CAPS and lymphoma relapsed, and the patient underwent autologous hematopoietic stem cell transplantation. Complete remission of the lymphoma has been successfully maintained, and the condition of the patient has remained stable for two years with no further evidence of thrombosis.