The benefits of transcranial direct current stimulation (tDCS) on brain function, cognitive response, and motor ability are well described in scientific literature. Nevertheless, the effects of tDCS on athletes’ performance remain unclear. To compare the acute effects of tDCS on the running performance of 5000 m (m) runners. Eighteen athletes were randomized into Anodal (n = 9) groups that received tDCS for 20 min and 2 mA, and Sham (n = 9), in the motor cortex region (M1). Running time in 5000 m, speed, perceived exertion (RPE), internal load and peak torque (Pt) were evaluated. The Shapiro–Wilk test followed by a paired Student’s t-test was used to compare Pt and total time to complete the run between the groups. The running time and speed of the Anodal group (p = 0.02; 95% CI 0.11–2.32; d = 1.24) was lower than the Sham group (p = 0.02, 95% CI 0.05–2.20; d = 1.15). However, no difference was found in Pt (p = 0.70; 95% CI − 0.75 to 1.11; d = 0.18), RPE (p = 0.23; 95% CI − 1.55 to 0.39; d = 0.60) and internal charge (p = 0.73; 95% CI − 0.77 to 1.09; d = 0.17). Our data indicate that tDCS can acutely optimize the time and speed of 5000 m runners. However, no alterations were found for Pt and RPE.