East Asia is the largest source region of global anthropogenic mercury emissions, and contributes to atmospheric mercury concentration and deposition in other regions. Similarly, mercury from the global pool also plays a role in the chemical transport of mercury in East Asia. Annual simulations of atmospheric mercury in East Asia were performed using the STEM-Hg modeling system to study the mass budgets of mercury in the region. The model results showed strong seasonal variation in mercury concentration and deposition, with signals from large point sources. The annual mean concentrations for gaseous elemental mercury, reactive gaseous mercury and particulate mercury in central China and eastern coastal areas were 1.8 ng m^− 3, 100 pg m^− 3 and 150 pg m^− 3, respectively. Boundary conditions had a strong influence on the simulated mercury concentration and deposition, contributing to 80% of the concentration and 70% of the deposition predicted by the model. The rest was caused by the regional emissions before they were transported out of the model domain. Using different oxidation rates reported for the Hg⁰–O₃ reaction (i.e., by Hall, 1995 vs. by Pal and Ariya, 2004) led to a 9% difference in the predicted mean concentration and a 40% difference in the predicted mean deposition. The estimated annual dry and wet deposition for East Asia in 2001 was in the range of 590–735 Mg and 482–696 Mg, respectively. The mercury mass outflow caused by the emissions in the domain was estimated to be 681–714 Mg yr^− 1. This constituted 70% of the total mercury emission in the domain. The greatest outflow occurred in spring and early summer.