Although several global/regional studies have detailed the high level of polycyclic aromatic hydrocarbons in urban areas worldwide, unfortunately, Nepal has never been part of any global/regional regular monitoring plan. Despite few sporadic studies exist, the systematic monitoring and integrated concentration of PAHs in urban region of Nepal are lacking. In this study, the concentrations, sources, and health risk assessment of 16 PAHs in air (n = 34) were investigated in suspected source areas/more densely populated regions of Nepal. Four potential source areas in Nepal were focused as it was conjectured that urban centers in plain areas (Birgunj and Biratnagar) would possibly be more influenced by PAHs as a result of intense biomass/crop residue burning than those in hilly areas (Kathmandu and Pokhara). The overall concentrations of ∑16PAHs ranged from 4.3 to 131 ng/m3 (median 33.3 ng/m3). ∑16PAH concentrations in plain areas were two folds higher than those in hilly areas. PHE was the most abundant followed by FLUA, PYR, and NAP, which accounted for 36%, 15%, 12%, and 9% of ∑16PAHs, respectively. Principal component analysis confirmed that PAHs in highly urbanized areas (Kathmandu and Pokhara) were related to diesel exhausts and coal combustion, while PAHs in less urbanized regions (Birgunj and Biratnagar) originated from biomass and domestic wood combustions. Furthermore, in the urban areas of Nepal, vehicular emission could also influence atmospheric PAHs. The lifetime cancer risk per million populations due to PAH exposures was estimated to be higher for plain areas than that for hilly areas, suggesting a relatively greater risk of cancer in people living in plain areas.