Abstract Background Cognitive impairment and cerebrovascular pathology are both frequent with ageing. Cognitive impairment due to vascular pathology of the brain, termed vascular cognitive impairment (VCI), is one of the most frequent causes of cognitive impairment in elderly subjects. Thus far, VCI has no specific pharmacological treatment. Recent observational studies have suggested a protective effect of physical activity in cognition, but adequate randomised controlled trials (RCT) are lacking. Methods AFIVASC is a multi-centre randomised controlled trial, with a 6-month intervention treatment and an additional follow-up of 6 months, that aims to estimate the impact of 6 months of moderate intensity physical activity on cognition (the primary outcome) at 6 and 12 months in subjects with VCI. Participants are community dwellers with criteria for VCI without dementia or who have had previous stroke or transient ischaemic attack (TIA). Patients may be self-referred or referred from a medical appointment. After confirming the inclusion criteria, a run-in period of 1 month is conducted to access adherence; only after that are subjects randomly assigned (using a computerised program blinded to clinical details) to two groups (intervention group and best practice usual care group). The intervention consists of three physical activity sessions of 60 min each (two supervised and one unsupervised) per week. The primary outcome is measured by the presence or absence of decline in cognitive status. Secondary outcomes include changes in neuro-cognitive measures, quality of life, and functional and motor status. Primary and secondary outcomes are evaluated at 6 and 12 months by investigators blinded to both intervention and randomisation. A required sample size of 280 subjects was estimated. Statistical analyses will include regression analysis with repeated measures. The study was approved by the Ethics Committee for Health of Centro Hospitalar de Lisboa Norte (ref. no. 1063/13) and by the Ethics Committee for Health of Centro Hospitalar do Porto CHP (ref. no. 2016.055(049-DEFI/048-CES)). Discussion We aim to show whether or not moderate physical activity has a beneficial impact on cognition, quality of life, motor, and functional status in people with vascular cognitive impairment, and to generate new insights on the applicability of implementing physical activity in this specific population. Trial Registration ClinicalTrials.gov, NCT03578614 July 6, 2018.