WAKE-UP is an investigator-initiated, multicentre, randomised, double-blind, placebo-controlled trial designed to test efficacy and safety of MRI-based intravenous thrombolysis in patients with wake-up stroke. Every year 1.5 million patients suffer a stroke in the EU. Up to 20% of stroke patients wake up with stroke symptoms. Currently these patients are excluded from thrombolysis which is the only approved specific treatment available for acute stroke. However, recently the potential of MRI to identify patients likely to be within a time-window for thrombolysis (≤4.5 hours) was demonstrated. WAKE-UP will use a specific MRI pattern, i.e. the mismatch between a visible lesion on diffusion weighted imaging (DWI) and a normal fluid attenuated inversion recovery (FLAIR) image, to randomise patients waking up with stroke symptoms to either treatment with Alteplase or placebo. The primary endpoint will be favourable outcome at 3 months. A total of 800 patients will be enrolled in 40 centres in six EU countries. Additional MRI information such as vessel occlusion or perfusion lesion will not be used for enrolment but will be studied as possible modifiers of the response to thrombolysis. Software will be developed to facilitate the processing and analysis of multiparametric stroke MRI and to assist the integration of modern stroke imaging into acute treatment decisions. The trial will be accompanied by activities increasing the awareness for acute stroke in the public and results will be disseminated within the scientific community as well as within the public. WAKE-UP is aimed to promote a paradigm-change in acute stroke treatment, and to provide effective treatment to a large new group of patients. The results of WAKE-UP are expected to change guidelines of acute stroke management and clinical practice. WAKE-UP will help to reduce the burden of stroke related disability in the EU.