We developed an index to investigate the effect of transboundary air pollution (TAP) on the air quality of Kumamoto City, Japan. We estimated the effect of TAP by using the index and positive matrix factorization (PMF). Polycyclic aromatic hydrocarbons (PAHs) and trace metals were analyzed from the daily samples of the Total Suspended Particles (TSPs) collected seasonally from Oct. 2014 to Aug. 2015. These chemical components exhibited high concentrations in spring and winter, which is consistent with the data in the literature. Pb was identified as the TAP tracer owing to its high concentrations in winter and spring. Indeno(1, 2, 3-cd)pyrene (IcdP) was used as the local emission tracer in Kumamoto on the basis of previous studies. We applied the IcdP/Pb ratio as the index. The index enables the detection of TAP in daily data sets. PMF identified six factors: soil and road dust, biomass and waste burning, heavy oil combustion, fishing boats, vehicle emission, and coal combustion. The average contribution of TAP on the days when transboundary pollution was high was evaluated as being 46%.