Refractory antiphospholipid syndrome represents a challenge for preventing thrombosis that may occur despite adequate anticoagulation and immunomodulation therapy. Here, we report a 35-year-old male patient who presented with variable venous thromboembolic events. Autologous hematopoietic stem cell transplant was performed after conditioning with cyclophosphamide and antithymocyte globulin. Five years after transplant, the treatment continued to show a successful outcome in preventing new thrombotic events. Autologous hematopoietic stem cell transplant represents a chance for cure from antiphospholipid syndrome despite the paucity of reported data so far.