Background Previous research has used the brain-computer interface (BCI) to promote upper-limb motor rehabilitation. However, the results of these studies were variable, leaving efficacy unclear. Objectives This review aims to evaluate the effects of BCI-based training on post-stroke upper-limb rehabilitation and identify potential factors that may affect the outcome. Design A meta-analysis including all available randomized-controlled clinical trials (RCTs) that reported the efficacy of BCI-based training on upper-limb motor rehabilitation after stroke. Data sources and methodsWe searched PubMed, Cochrane Library, and Web of Science before September 15, 2024, for relevant studies. The primary efficacy outcome was the Fugl-Meyer Assessment-Upper extremity (FMA-UE). RevMan 5.4.1 with a random effect model was used for data synthesis and analysis. Mean difference (MD) and 95% confidence interval (95%CI) were calculated. Results Twenty-one RCTs (n = 886 patients) were reviewed in the meta-analysis. Compared with control, BCI-based training exerted significant effects on FMA-UE (MD = 3.69, 95%CI 2.41-4.96, P < 0.00001, moderate-quality evidence), Wolf Motor Function Test (WMFT) (MD = 5.00, 95%CI 2.14-7.86, P = 0.0006, low-quality evidence), and Action Research Arm Test (ARAT) (MD = 2.04, 95%CI 0.25-3.82, P = 0.03, high-quality evidence). Additionally, BCI-based training was effective on FMA-UE for both subacute (MD = 4.24, 95%CI 1.81-6.67, P = 0.0006) and chronic patients (MD = 2.63, 95%CI 1.50-3.76, P < 0.00001). BCI combined with functional electrical stimulation (FES) (MD = 4.37, 95%CI 3.09-5.65, P < 0.00001), robots (MD = 2.87, 95%CI 0.69-5.04, P = 0.010), and visual feedback (MD = 4.46, 95%CI 0.24-8.68, P = 0.04) exhibited significant effects on FMA-UE. BCI combined with FES significantly improved FMA-UE for both subacute (MD = 5.31, 95%CI 2.58-8.03, P = 0.0001) and chronic patients (MD = 3.71, 95%CI 2.44-4.98, P < 0.00001), and BCI combined with robots was effective for chronic patients (MD = 1.60, 95%CI 0.15-3.05, P = 0.03). Better results may be achieved with daily training sessions ranging from 20 to 90 min, conducted 2-5 sessions per week for 3-4 weeks. Conclusions BCI-based training may be a reliable rehabilitation program to improve upper-limb motor impairment and function. Trial registration PROSPERO registration ID: CRD42022383390.