Introduction Compared to healthy individuals, stroke patients have five times the rate of dementia diagnosis within three years. Aerobic exercise may induce neuroprotective mechanisms that help to preserve, and even increase, brain volume and cognition. We seek to determine whether aerobic fitness training helps to protect brain volume and cognitive function after stroke compared to an active, non-aerobic control. Methods In this Phase IIb, single blind, randomised controlled trial, 100 ischaemic stroke participants, recruited at two months post-stroke, will be randomly allocated to either the intervention (aerobic and strength exercise) or active control (stretching and balance training). Participants will attend one-hour, individualised exercise sessions, three days-per-week for eight weeks. Assessments at two months (baseline), four months (post-intervention), and one year (follow-up) post-stroke will measure brain volume, cognition, mood, cardiorespiratory fitness, physical activity, blood pressure and blood biomarkers. Study outcome: Our primary outcome measure is hippocampal volume at four months after stroke. We hypothesise that participants who undertake the prescribed intervention will have preserved hippocampal volume at four months compared to the control group. We also hypothesise that this group will have preserved total brain volume and cognition, better mood, fitness, and higher levels of physical activity, than those receiving stretching and balance training. Discussion The promise of exercise training to prevent, or slow, the accelerated rates of brain atrophy and cognitive decline experienced by stroke survivors needs to be tested. Post Ischaemic Stroke Cardiovascular Exercise Study has the potential, if proven efficacious, to identify a new treatment that could be readily translated to the clinic.