Mercury (Hg) is a globally distributed heavy metal. Here, we study Hg concentration and isotopic composition to understand the status of Hg pollution and its sources in Pakistan's paddy soil. The collected paddy soils (n = 500) across the country have an average THg concentration of 22.30 ± 21.74 ng/g. This low mean concentration suggests Hg pollution in Pakistan was not as severe as previously thought. Meanwhile, samples collected near brick kilns and industrial areas were significantly higher in THg than others, suggesting the influence of Hg emitted from point sources in certain areas. Soil physicochemical properties showed typical characteristic of mineral soils due to the study area's arid to semi-arid climate. Hg stable isotopes analysis, depicted mean Δ¹⁹⁹Hg of −0.05 ± 0.12‰ and mean δ²⁰²Hg −0.45 ± 0.35‰, respectively, for contaminated sites, depicting Hg was primarily sourced from coal combustion by local anthropogenic sources. While uncontaminated sites show mean Δ¹⁹⁹Hg of 0.15 ± 0.08‰, mean Δ²⁰⁰Hg of 0.06 ± 0.07‰ and mean δ²⁰²Hg of −0.32 ± 0.28‰, implying long-range transboundry Hg transport through wet Hg(II) deposition as a dominant Hg source. This study fills a significant knowledge gap regarding the Hg pollution status in Pakistan and suggests that the Hg risk in Pakistan paddies is generally low.