Khaidarkan, Batken Province, Kyrgyzstan is home to one of the world’s largest and last primary mercury mines. Doctors without Borders (MSF) and the Ministry of Health (MOH) of Kyrgyzstan have found that the Batken region has an elevated rate of non-communicable diseases (NCD) within the country. NCD can be caused by environmental pollution. A human health risk assessment was conducted to investigate heavy metal exposure. Using a hand-held X-ray fluorescence (XRF) spectrometer for soil screening is faster and less expensive than reliance on bench-scale methods. To establish a site-specific mercury conversion factor between XRF and the local MOH lab’s Atomic Absorption Spectrometry (AAS) with a Pyrolyzer attachment, soil samples were collected in Khaidarkan and surrounding villages. Samples were analyzed by XRF in three stages: in situ, ex situ-bulk, and ex situ-sieved. The ex situ-sieved samples were analyzed by AAS. Analysis results indicate that in situ readings can be used as a qualitative tool for screening, and a conversion factor of 1.7 was most appropriate for converting ex situ-bulk/ex situ-sieved and AAS results. This analysis enables the MOH laboratory and others to use XRF as a quick and cost-effective monitoring tool for Hg contamination in soil.