Ischaemic stroke is one of the most common diseases world-wide. Recent studies provide new insights into the role of ATP-binding cassette (ABC) transporters in brain ischaemia. Expressional and functional transporter changes that have been observed at the brain capillary endothelium during ischaemia impede the access of pharmacological compounds into the brain tissue. The current review summarizes the most important findings and discusses the role of hypoxia, inflammation, oxidative stress and lipids as factors regulating ABC transporters at the blood-brain barrier. A better understanding of biodistribution processes at the blood-brain barrier is urgently needed, so that the accumulation of drugs in the brain can be improved, enabling a successful translation of pharmacological treatments in ischaemic stroke.