Anthropogenic sulfur compounds play an important role in acid deposition, aerosol particle formation, and subsequent radiative forcing and human fine particulate exposure. There are substantial uncertainties in processes influencing sulfate and precursor distributions, however, that have not yet been resolved through comparisons with observations. We find here an underappreciated factor that has a large impact on model results: uncertain emission height. Global aerosol‐climate model simulations indicate that the assumed effective anthropogenic emission height is very important to SO2 near‐surface concentrations and vertical profile. The global range of near‐surface SO2 concentration over land (ocean) due to uncertainty in industrial (international shipping) emission injection height is 81% (76%), relative to the average concentration. This sensitivity is much larger than the uncertainty of SO2 emission rates. Black carbon and primary organic matter concentration and profiles are also sensitive to emission heights (53% over land and 28% over oceans). The impact of emission height uncertainty is larger in winter for land‐based emissions, but larger in summer over the Northern Hemisphere ocean for shipping emissions. The variation in aerosol optical depth related to shipping emission injection heights is 11% over oceans, revealing the potential importance of injection height on aerosol forcing and climatic effects. The large impact on SO2 concentrations can confound attempts to use surface, aircraft, and satellite observations to constrain the importance of other processes that govern sulfur compound distributions in the atmosphere. The influence of emission height on vertical SO2 column also will impact the accuracy of satellite retrievals.