Fossil energy burning is one of the most important sources of atmospheric mercury emissions, which poses great threats to both environment and human health. Urban regions are dominant energy consumers; however, the information on the resultant mercury emissions in urban regions has been lacking. Therefore, in light of environmentally extended input-output analysis, this study used Beijing as a case to investigate embodied (direct plus indirect) mercury emissions induced by fossil energy consumption in urban regions. The results show that embodied mercury emissions caused by Beijing׳s fossil energy consumption amounted to 5.86 tonnes, which is over 1.5 times the direct emissions, indicating that the conventional direct emission accounting method will lead to significant emission leakage. Coal combustion takes the major responsibility for energy-related mercury emissions. As a net importer of embodied mercury emissions, Beijing avoided a considerable amount of mercury emissions. Sectors like construction which play key role in embodied mercury emissions are also identified in this study. To comprehensively reduce mercury emissions from energy consumption the Beijing government should devote efforts to develop clean coal technology and high efficiency mercury removal devices, shift investment from infrastructure construction to tertiary industries and optimize green consumption among the residents, especially the urban residents. The method and findings may be useful for compilation of overall urban mercury emissions inventory as well as have important policy implications for global cities to control mercury emissions.