Rationale Molecular hydrogen (H 2 ) is an important gas for atmospheric chemistry, and an indirect greenhouse gas due to its reaction with OH. The isotopic composition of H 2 (δD) has been used to investigate its atmospheric budget; here we add a new observable, the clumped isotopic signature ΔDD, to the tools that can be used to study the global cycle of H 2 . Methods A method for determining ΔDD in H 2 was developed using the high‐resolution MAT 253‐Ultra isotope ratio mass spectrometer (Thermo Fisher). The HH, HD and DD abundances are quantified at medium resolution (M/ΔM ≈ 6000), which is sufficient for HD + and DD + to be distinguished from H 3 + and H 2 D + , respectively. The method involves sequential measurement of isotopologues, and DD is measured using an ion counter. For verification, catalytic ΔDD equilibration experiments were performed at temperatures of up to 850°C. Results The typical precision obtained for ΔDD is 2–6‰, close to the theoretical counting statistics limit, and adequate for detecting the expected natural variations. Compatibility and medium‐term reproducibility are consistent with the precision values. The method was validated using temperature equilibration experiments, which showed a dependence of ΔDD on temperature as expected form theoretical calculations. Conclusions We have established a method for determining ΔDD in H 2 at natural isotopic abundances, with a precision that is adequate for observing the expected variations in atmospheric and other natural H 2 . This method opens the road to new research on the natural H 2 cycle.