The standard treatment of thrombotic antiphospholipid syndrome (APS) is lifelong oral anticoagulation with a vitamin K antagonist (VKA), generally warfarin. A minority of APS patients re-thrombose despite seemingly adequate anticoagulation. These patients are deemed anticoagulant-refractory. The management of anticoagulant-refractory APS is largely empirical and extrapolated from other clinically similar situations. Further options include increased VKA anticoagulation intensity or alternative antithrombotic strategies, including low-molecular-weight heparin, fondaparinux, the addition of antiplatelet therapy and consideration of vascular options. Anticoagulant-refractory thrombotic APS patients may have APS-associated thrombocytopenia, which necessitates balancing the risk of recurrent thrombosis versus bleeding, to achieve adequate anticoagulation. The multiple mechanisms involved in the generation of the thrombotic phenotype in APS suggest that anticoagulation alone may not control thrombosis. Thus, other modalities, including adjunctive treatment (hydroxychloroquine, statins and vitamin D) for APS-related thrombosis merit consideration, as well as immunomodulatory therapy and complement inhibition. APS patients may have coexistent systemic lupus erythematosus, which adds to the complexity of managing their thromboembolic disease. However, with attention to detail and judicious application of the limited data, it is possible to minimise the morbidity resulting from anticoagulant-refractory thrombotic APS. Multicentre studies are required to guide the sequence of interventions and their comparative efficacy in patients with anticoagulant-refractory thrombotic APS.