Aircrafts enable the direct measurement of chemical components in the free troposphere (FT). This study employed airborne measurements to examine the occurrences of high concentrations of SO2 and NOx in the FT over the coastal region west of the Seoul metropolitan area, South Korea. The data from a long-term (1997–2011) airborne measurement campaign were used to determine the meteorological conditions favorable for carrying these pollutants into the Seoul area. The back trajectory analyses of 21 instances of high FT pollutant concentration events showed ascending patterns from the major pollutant sources, mainly the industrial complexes in eastern China, in 9 instances and passing patterns in 12 instances. In the ascending instances, developing low-pressure systems over the source regions provide favorable conditions to uplift air pollutants from the surface into the FT. In the passing instances, an anomalous low-pressure system near the surface prevented airflows from descending into the boundary layer and upper-level anticyclonic systems helped to keep the ascending airflows in the FT. This study proposes the basic mechanisms for predicting air quality in the Seoul area, considering that air pollutants in the FT often entrain into the boundary layer to increase local concentrations.