<p>Deuterium labelling has widespread applications in medicinal chemistry, chemical science and materials science. Hydrogen isotope exchange for deuterium labelling of C(<i>sp</i>³)–H bonds under mild conditions remains a key challenge in labelling reactions. Here we show an electrocatalytic strategy enabling rapid (&lt;10 min) deuteration of natural products and pharmaceuticals. Using clusters containing boron, (TBA)₂B₁₀H₁₀, as the electrocatalyst, anodically generated [B₁₀H₁₀]^•− intermediates undergo hydrogen-atom transfer with C(<i>sp</i>³)–H/D bonds, forming stabilized [B₁₀H₁₀H/D]⁻ species. Cathodic reduction then triggers selective H/D exchange with carbon radicals, regenerating the catalyst. The boron cluster modulates reactive H/D radicals via reversible electron transfer, balancing radical activity and stability to enable efficient labelling without harsh reagents. This method achieves broad substrate compatibility and high deuterium incorporation and is demonstrated using complex drug molecules. By integrating electrocatalysis with boron cluster-mediated hydrogen-atom transfer, we provide a general platform for C(<i>sp</i>³)–H deuteration, advancing isotope-labelling applications in synthetic and medicinal chemistry.</p><p></p>