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. 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. 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. We 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. 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. BCI-based training may be a reliable rehabilitation program to improve upper-limb motor impairment and function. PROSPERO registration ID: CRD42022383390.