The development of non-noble metal and earth-abundant-based electrocatalysts for electrochemical hydrogen production is of great significance for large scale application of water splitting technology. Particularly, molybdenum- and tungsten-based materials, such as MoS2, WS2, MoP, and WP, are widely studied for their promising performance in catalyzing the hydrogen evolution reaction (HER), especially in their nanostructured forms. Here, we investigate the HER activity of nanostructured molybdenum and tungsten borides, which are highly understudied, and report the use of bipolar electrochemistry (BP) to enhance their performances. BP treatment induces the size reduction of commercial Mo2B5 and W2B5 from the micrometer range down to the nanometer range. The smaller Mo2B5 and W2B5 particles have greater exposure of active sites for HER catalysis and result in better HER performance. To illustrate, we found that the electrocatalytic performance of BP-treated W2B5 is close to the best HER electrocatalyst, Pt/C. Electrochemical impedance spectroscopy measurements reveal lower charge transfer resistance (Rct) of the materials after bipolar electrochemical treatment, thereby suggesting another effect of the BP method in enhancing HER catalysis. Overall, we demonstrate bipolar electrochemistry as a simple method to improve the catalytic activity of Mo2B5 and W2B5.