Background It is known that repetitive, skilled, functional movement is beneficial in driving functional reorganisation of the brain early after stroke. This study will investigate a) whether pedalling an upright, static exercise cycle, to provide such beneficial activity, will enhance recovery and b) which stroke survivors might be able to participate in pedalling. Methods/Design Participants (n = 24) will be up to 30 days since stroke onset, with unilateral weakness and unable to walk without assistance. This study will use a modified exercise bicycle fitted with a UniCam crank. All participants will give informed consent, then undergo baseline measurements, and then attempt to pedal. Those able to pedal will be entered into a single-centre, observer-blinded randomised controlled trial (RCT). All participants will receive routine rehabilitation. The experimental group will, in addition, pedal daily for up to ten minutes, for up to ten working days. Prognostic indicators, measured at baseline, will be: site of stroke lesion, trunk control, ability to ambulate, and severity of lower limb paresis. The primary outcome for the RCT is ability to voluntarily contract paretic lower limb muscle, measured by the Motricity Index. Secondary outcomes include ability to ambulate and timing of onset and offset of activity in antagonist muscle groups during pedalling, measured by EMG. Discussion This protocol is for a trial of a novel therapy intervention. Findings will establish whether there is sufficient evidence of benefit to justify proceeding with further research into clinical efficacy of upright pedalling exercise early after stroke. Information on potential prognostic indicators will suggest which stroke survivors could benefit from the intervention.