Antithrombotic therapy is a key element of secondary prevention in patients who have had an ischaemic stroke or transient ischaemic attack. However, its use in clinical practice is not always straightforward. This review provides an update on certain difficult scenarios in antithrombotic management, with a focus on recent clinical trials and large observational studies. We discuss the approach to patients with an indication for antithrombotic treatment who also have clinical or radiological evidence of previous intracranial bleeding, patients with indications for both anticoagulant and antiplatelet treatment, and patients in whom antithrombotic treatment fails to prevent stroke. We also review the timing of anticoagulation initiation after cardioembolic stroke, and the use of antithrombotics in patients with asymptomatic cerebrovascular disease. Despite a wealth of new evidence, numerous uncertainties remain and we highlight ongoing trials addressing these.