Acquired amegakaryocytic thrombocytopenia (AAMT) is a rare cause of thrombocytopenia seen in systemic lupus erythematosus (SLE) that is frequently misdiagnosed as immune thrombocytopenic purpura (ITP). Often patients do not respond to standard ITP treatment. Prompt bone marrow biopsy and further workup should ensue as it is a diagnosis of exclusion. While no standard guidelines exist, the mainstay of treatment is immunosuppressive therapy. Some cases are refractory and should have a follow-up biopsy, typically showing worsening disease. The exact pathogenesis is unclear; multiple mechanisms may be involved, suggesting AAMT may be a syndrome of various aetiologies rather than a distinct pathology. A common complication is aplastic anaemia, and the patient may need a haematopoietic stem cell transplant (HSCT). We present a young man with severe refractory AAMT in the setting of SLE that progressed to aplastic anaemia and required an HSCT. We then discuss and interpret the literature on AAMT.