introductionRehabilitation is recognised as a cornerstone of recovery in the stroke care pathway, and the intensity of therapy is closely related to functional recovery. However, longitudinal studies investigating differences in short- and long-term outcomes between ischaemic and haemorrhagic strokes remain scarce. In particular, it is not yet clear whether atrial fibrillation-related stroke (AFRS) entails specific rehabilitation needs or leads to different functional outcomes compared with non-AFRS. Identifying aetiology-specific recovery patterns may support the development of predictive models of stroke recovery and optimise the use of rehabilitation resources. METHODS AND ANALYSIS: In this prospective observational cohort study, patients with stroke will be recruited from the Stroke Unit of a tertiary hospital. Patients discharged from the unit who require inpatient rehabilitation will be allocated to one of two rehabilitation centres offering programmes of differing intensity: high-intensity (three to five sessions daily) or moderate-intensity (one to two sessions daily). Allocation criteria are based on standard clinical parameters, including age, prior functional level, neurological impairment and cognitive and medical status. The primary outcome is functional recovery, measured using the Barthel Index at 6 months post-stroke. Rehabilitation needs, the time course of disability and final outcomes will be compared between AFRS and non-AFRS groups. ETHICS AND DISSEMINATION: The study has received approval from the local Research Ethics Committee of Hospital del Mar, Barcelona, Catalonia, Spain (Ref. 2023/11172/I). Written informed consent will be obtained from all participants prior to inclusion. Study findings will be disseminated through peer-reviewed publications, conference presentations and communication activities aligned with the TARGET project dissemination strategy. TRIAL REGISTRATION NUMBER: NCT07253974.