To investigate the effect of a 6-week stroboscopic balance training program on cortical activities in athletes with chronic ankle instability. Randomized controlled trial. Setting: Single-center. Thirty-nine participants were assigned to the strobe group (SG, n = 13), non-strobe group (NSG, n = 13), and control group (CG, n = 13). Cortical activity and balance velocity were evaluated while the athletes were on the HUBER balance device. Electroencephalographic measurements of cortical activity were made at the transition from bipedal stance to single-leg stance. The SG showed significant increases in Cz theta and alpha values and COP-v (center of pressure velocity) between pretest and posttest (p < 0.001, p = 0.003, p < 0.001). Posttest Cz theta was significantly higher in the SG compared to the CG (p = 0.009) and posttest Cz alpha was significantly higher in the SG compared to the NSG (p = 0.039) and CG (p = 0.001). Posttest COP-v was significantly higher in the SG than in the CG (p = 0.031) and NSG (p = 0.03). Stroboscopic training may be clinically beneficial to improve balance parameters in athletes with CAI, and may have utility in sport-specific activity phases of rehabilitation to reduce visual input and increase motor control. •Strobe training increases theta and alpha waves on cortical activities.•Strobe training increases center of pressure velocity.•Stroboscopic training can be used to enhance traditional balance training.