Background: Stroke is a leading cause of neurological disability worldwide, with upper limb impairment affecting approximately 70% of survivors and only 5–20% achieving complete dexterity recovery at six months. Brain–computer interface (BCI) neurorehabilitation decodes motor intentions from electroencephalographic (EEG) signals to deliver synchronized functional electrical stimulation (FES) and virtual reality feedback, creating a closed-loop neurofeedback system that reinforces motor learning. While existing evidence supports BCI efficacy and safety in chronic stroke, its feasibility, safety, and cost-effectiveness during the acute and subacute phase (2 to 12 weeks post-stroke), when neuroplasticity is heightened, remain underexplored. Furthermore, there is a paucity of data regarding preliminary health economic analyses for BCI rehabilitation in acute stroke rehabilitation settings. Methods: This prospective, open-label, single-arm pragmatic feasibility pilot trial will recruit 12 patients with hemorrhagic or ischemic stroke (2–12 weeks post-stroke) undergoing inpatient rehabilitation from a public healthcare institution. Up to 15 sessions of BCI-rehabilitation of 30 min each using the recoveriX system will be supervised by a trained therapist or clinical research assistant (4–5 sessions/week over 3–4 weeks), followed by standard occupational therapy within 30–60 min of BCI-rehabilitation. Primary outcomes assessing feasibility and adherence include eligibility and recruitment rate (%/screened); tolerability using self-rated System Usability Scale (SUS) score; within-session adherence > 80%/240 trials, summated for completed trials per patient; programme completion number > 80% of scheduled (>12/15) sessions; and training-related adverse events per patient ≤ 17% (≤2/12 sessions). Secondary outcome measures include clinical efficacy by arm impairment scale using hemiplegic Upper Limb Fugl–Meyer Motor Assessment (FMA-UE), hand function using Action Research Arm Test (ARAT), admission and discharge functional status (Functional Independence Measure-FIM (18–126), Modified Barthel Index-MBI (0–100), stroke impact scale (SIS_3.0), arm, participation domains), and economic analysis. All outcomes will be measured by trained therapists/researchers at baseline week 0, week 3–4 (post-BCI-rehabilitation), and week 12 and 24 (follow-up). BCI-rehabilitation EEG-derived electrophysiological correlates of recovery will be extracted to better understand participant progress over time. An incremental cost-utility analysis will compare the BCI-rehabilitation participants against propensity-matched historical controls from the TTSH stroke rehabilitation registry (2017 to 2025), stratified by baseline motor severity. Discussion: This study will provide preliminary evidence on feasibility, tolerability, safety, clinical efficacy, and cost-effectiveness of early BCI-rehabilitation in acute/subacute stroke to better inform clinicians on its implementation.