Lysosomial diseases and autoimmune diseases are systemic disorders. Their clinical manifestations can overlap with the broad spectrum of one another. Their association has been rarely reported. We report a new case of systemic lupus erythematous (SLE) associated to antiphospholipid syndrome (APS) and Hashimoto thyroiditis occurring in Niemann-Pick disease (NPD) type B patient. A 42-year-old woman with a familial history of NPD was diagnosed with a NPD type B at the age of ten. Twenty years later (2008), she complained of inflammatory arthralgia with acute dyspnea. She was diagnosed with SLE (according to ACR criteria) and Hashimoto disease with positive IgG anti-cardiolipin and IgA anti-beta2 glycoprotein. In 2018, she presented a left segmental pulmonary embolism. Antiphospholipid syndrome was retained. She was treated with steroids, hydroxychloroquine, anticoagulation therapy and levothyroxine. Her SLE treatment was re-enforced by cyclophosphamide because of corticosteroid dependence and recurrent hemolytic crises.