Triple negative breast cancer (TNBC) relapses more frequently then hormone receptor-positive subtypes and is often associated with poor outcomes. This is due to the fact that TNBC is more likely to spread to the brain, where current management strategies do not drastically alter outcomes. Indeed the overall survival for patients with a diagnosis of brain metastases is 4.3 months. Therefore, there is an urgent requirement for better therapeutic strategies. Having generated chemical antibodies against the cell surface marker, EpCAM, we sought to functionalise this aptamer to target brain metastases. A recent development has shown that targeting the transferrin receptor on the blood brain barrier can transport molecules into the brain via receptor-mediated transcytosis. We have generated a chemical antibody to the transferrin receptor and demonstrated that it can indeed enter the brain in an in vivo mouse model. Indeed, this aptamer specifically entered the brain within 10 minutes of tail vein injection. We have attached a second chemical antibody, targeting EpCAM, to this transcytosing aptamer and confirmed its specificity and sensitivity using flow cytometry against transferrin receptor positive or negative cell lines, as well as EpCAM positive or negative cells lines. Furthermore, we have shown that it is specifically internalized via receptor-mediated endocytosis into MDA-MB-231 cells. As well, we have attached the common chemotherapeutic, doxorubicin, to this bi-functional aptamer, and demonstrated that it is specifically internalized within the targeted cells. These results demonstrate that this bi-functional aptamer-doxorubicin conjugate has potential for the specific targeting and treatment of brain metastases in TNBC patients. Moreover, by specifically targeting the cancer cells in the brain, this novel modality is likely to mitigate the neurotoxic effects of chemotherapeutic agents on the healthy brain tissue.