Scorpion fauna of Mongolia, which are thus far poorly understood, were investigated country-wide during a China-Mongolia joint field survey from 2009 to 2012. Of the total 134 sites we surveyed, scorpions were found at 10 sites in the southern Gobi regions, Umnugovi and Dornogovi Aimags (Provinces) of Mongolia. All scorpions collected from Mongolia belong to a single species, Mesobuthus eupeus mongolicus. Combining with its occurrence records in China, we assembled 98 presence data for M. eupeus mongolicus and predicted its geographical distribution using ecological niche modeling approach. This species occurs exclusively in the arid deserts and steppes, ranging from the west extreme of Junggar Basin (Xinjiang) to the Gobi deserts in North China and South Mongolia, with its distributional margins set by the Altai Mountains in the north, the Tian-Shan Mountains and the Qinghai-Tibet Plateau in the south, and the Loess Plateau in the east. We found that ecological niche models could accurately predict (AUC = 0.880 ± 0.016) geographic distribution of M. eupeus mongolicus. Our results show that climate is a reliable predictor for the geographic range of M. eupeus mongolicus, implying that climate might have exerted a dominant control over the natural occurrence of this species. A brief note on the ecology of M. eupeus mongolicus was also provided.