(1) Background: Balance decline is highly prevalent in people suffering from chronic ankle instability (CAI). The control of balance depends upon multiple neurophysiologic systems including the activation of cortical brain regions (e.g., the primary sensorimotor cortex). The excitability of this region, however, is diminished in people with CAI. In this pilot double-blinded randomized controlled trial, we tested the effects of high-definition transcranial direct current stimulation (HD-tDCS) designed to facilitate the excitability of M1 and S1 in combination with short-foot exercise (SFE) training on proprioception and dynamic balance performance in individuals with CAI. (2) Methods: Thirty young adults completed baseline assessments including the Active Movement Extent Discrimination Apparatus (AMEDA), Joint Position Reproduction (JPR) test, Y-balance test, and the Sensory Organization Test (SOT). They were then randomized to receive a four-week intervention of SFE in combination with tDCS (i.e., HD-tDCS+SFE) or sham (i.e., control) stimulation. Baseline assessments were repeated once-weekly throughout the intervention and during a two-week follow-up period. (3) Results: Twenty-eight participants completed this study. Blinding procedures were successful and no adverse events were reported. As compared to the control group, the HD-tDCS+SFE group exhibited significant improvements in the JPR test, the Y balance test, and the SOT at different time points. No group by time interaction was observed in AMEDA test performance. (4) Conclusions: HD-tDCS combined with SFE may improve dynamic balance and proprioception in CAI. Larger, more definitive trials with extended follow-up are warranted.