Metastatic brain tumours occur in approximately 25% of all cancer patients following primary malignancy treatment. Protected by the body’s most formidable barrier, the blood brain barrier (BBB), treatment options for patients is limited and thus prognosis is poor, with survival time measured in months. A promising new approach toward by-passing this barrier, is to hijack active transport mechanisms present on the endothelial cell membranes, in particular the transferrin receptor (TfR). Nucleic acid based aptamers are ideal for this purpose given the ability to generate them against a vast range of targets, their stability and safety profile. This study aims to generate a bi-functional aptamer which can transcytose the BBB by targeting the TfR and specifically delivering a cytotoxic payload to the tumours. To achieve this, a 14-mer DNA aptamer against the TfR was joined to a 19-mer DNA aptamer targeting EpCAM, a glycoprotein overexpressed in a number of solid tumours with a high incidence of metastasing to the brain. The specificity and selectivity of these aptamers was confirmed against a number of cells lines expressing the TfR, EpCAM or neither protein, using flow cytometry and confocal microscopy. The ability of this aptamer to enter the brain in a living system has been demonstrative using an in vivo mouse model, with the results showing specific internalisation within 10 minutes following tail vein injection. Intercalation of the common chemotherapeutic doxorubicin, showed no influence on aptamer specificity, with the conjugate specifically internalised within the targeted cells following one hour incubation. These results demonstrate the great potential this bi-functional aptamer doxorubicin conjugate has for the specific treatment of brain metastases, which will improve patient survival and quality of life, in addition to the possibility of mitigating the neurotoxic effects on healthy brain tissue.