Long-range atmospheric transport (LRAT) plays a crucial role in the occurrence of persistent organic pollutants (POPs) in remote regions. When studying the LRAT of POPs on the Tibetan Plateau, westerly-controlled regions have received insufficient attention compared with regions influenced by the Indian monsoon or air flow from East Asia. We investigated the residual levels of POPs in soils from the eastern Pamirs and used air backward trajectory analysis to elucidate the influence of potential source regions via LRAT. Organochlorine pesticides (OCPs, mainly comprising DDTs, HCHs, and HCB), polychlorinated biphenyls (PCBs, mainly comprising penta- and hexa-CBs), and polycyclic aromatic hydrocarbons (PAHs, mainly comprising three- and four-ring) were detected at low concentrations of 40–1000, <MDL–88, and 2100–34,000 pg/g, respectively. We elucidated three major geographical distribution patterns of POPs, which were influenced by (1) the distribution of total organic carbon and black carbon in soil, (2) historical use of pesticides in the Tarim Basin, and (3) continuous emissions. Central Asia and the Tarim Basin were major potential source regions of POPs reaching the eastern Pamirs via LRAT. Historical use of technical HCH or lindane and technical DDT in potential source regions may contribute to the accumulation of HCHs and DDTs in the eastern Pamirs, respectively. Local sources seem to play a more important role in the occurrence of PAHs in the study area. By being under the control of less contaminated westerly air flow, the eastern Pamirs are more pristine than the core of the Tibetan Plateau where the Indian and East Asia monsoons deliver contaminants from highly industrialized areas in East China and India.