Polychlorinated naphthalenes (PCNs) are now under review by the Stockholm Convention as candidates for persistent organic pollutants (POPs) due to their persistence, toxicity, bioaccumulation, and long-range atmospheric transport. Data on PCN levels are sparse in South Asia. Atmospheric PCNs in India and Pakistan were monitored during the winter by polyurethane foam disk passive air samplers (PUF-PAS). The average concentrations were 29 pg/m3 and 7.7 pg/m3 in the Indian and Pakistani samples, respectively. Those concentration levels were relatively lower than the previously reported values in other Asian countries, but still considerably higher than in other sites in the world. Tri-CNs and tetra-CNs were the dominant homologues in the air, especially in India. Spatially, the PCNs were ubiquitous in the target areas, and local distribution was generally impacted by the proximity to potential sources. Major sources of PCNs in this study were the re-emission of Halowax and industrial thermal processes. Biomass burning influenced some sites in Pakistan. However, the enrichment of tri-CNs in Indian cities cannot be ascribed to either the signature of a specific source or the preferential volatilization and/or photodegradation in tropical areas. Despite this unclear issue in South Asia, the present study indicates that the potential health impact was generally comparable to that in non-urban sites worldwide.