In this study, we aim to determine the correlation between the height of the atmospheric boundary layer (ABL) and the concentrations of polybrominated diphenyl ether (PBDE) congeners, in an effort to improve comprehension of the atmospheric behavior of PBDEs. We used the PBDE data in air (n = 298), which were measured by the Japan Ministry of Environment (JMOE) at 50 sites across Japan during the period 2009-2012. The height of the ABL, which directly affects the PBDE concentrations in the near-surface air, was estimated by employing data retrieved from the Japanese global reanalysis (JRA-55) database, using the parcel and Richardson number method. The ABL has shown a strong inverse relationship with BDE-47 and BDE-99 (p < 0.01). In contrast, there was less correlation between BDE-209 and the ABL (p = 0.258). These differing behaviors could be explained by differences in particle size distribution of PBDEs, where BDE-47 and BDE-99 are associated with gas phases and fine particles and BDE-209 is associated with coarse particles. To our knowledge, this paper represents the first large-scale analysis of correlations between the ABL and the concentrations of PBDEs in the air.