This study presents a new steady-state visual evoked potential (SSVEP)-based brain–machine interface (BMI) using flickering visual stimuli at frequencies greater than the critical flicker frequency (CFF).We first asked participants to fixate on a green/blue flicker (30–70Hz), and SSVEP amplitude was evaluated. Participants were asked to indicate whether the stimulus was visibly flickering and to report their subjective level of discomfort. We then assessed visibly (41, 43, and 45Hz) vs. invisibly (61, 63, and 65Hz) flickering stimulus in an SSVEP-based BMI. Visual fatigue was assessed via the flicker test before and after operation of the BMI.Higher frequency stimuli reduced participants’ subjective discomfort. Participants successfully controlled the SSVEP-based BMI using both the visibly and invisibly flickering stimuli (93.1% and 88.0%, respectively); the flicker test revealed a decrease in CFF (i.e., visual fatigue) under the visible condition only (–5.7%, P<0.001).The use of high-frequency visual stimuli above the CFF led to high classification accuracy and decreased visual fatigue in an SSVEP-based BMI.High-frequency flicker stimuli above the CFF were able to induce SSVEPs and may prove useful in the development of BMI-based assistive products.