The global tropospheric distribution of molecular hydrogen (H<sub>2</sub>) and its uptake by the soil are simulated using a model called CHemical AGCM (atmospheric general circulation model) for the Study of the Environment and Radiative forcing (CHASER), which incorporates a two-layered soil diffusion/uptake process component. The simulated distribution of deposition velocity over land is influenced by regional climate, and has a global average of 3.3×10<sup>−2</sup> cm s<sup>−1</sup>. In the region north of 30° N, the amount of soil uptake shows a large seasonal variation corresponding to change in biological activity due to soil temperature and change in diffusion suppression by snow cover. In the temperate and humid regions in the mid- to low- latitudes, the uptake is mostly influenced by the soil air ratio, which controls the gas diffusivity in the soil. In the semi-arid regions, water stress and high temperatures contribute to the reduction of biological activity, as well as to the seasonal variation in the deposition velocity. A comparison with the observations shows that the model reproduces both the distribution and seasonal variation of H<sub>2</sub> relatively well. The global burden and tropospheric lifetime of H<sub>2</sub> are 150 Tg and 2.0 yr, respectively. The seasonal variation in H<sub>2</sub> mixing ratios at the northern high latitudes is mainly controlled by a large seasonal change in the soil uptake. In the Southern Hemisphere, seasonal change in net chemical production and inter-hemispheric transport are the dominant causes of the seasonal cycle, while large biomass burning contributes significantly to the seasonal variation in the tropics and subtropics. Both observations and the model show large inter-annual variations, especially for the period 1997–1998, associated with large biomass burning in the tropics and at Northern Hemisphere high latitudes. The soil uptake shows relatively small inter-annual variability compared with the biomass burning signal. Given that the thickness of biologically inactive layer plays an important role in the soil uptake of H<sub>2</sub>, its value in the model is chosen to achieve agreement with the observed H<sub>2</sub> trends. Uncertainty of the estimated soil uptake flux in the semi-arid region is still large, reflecting the discrepancy in the observed and modeled seasonal variations.