This paper presents a study conducted in São Paulo, Brazil, where the planetary boundary layer height (PBLH) was determined using ceilometer data and the wavelet covariance transform method. The retrieved PBLH values were subsequently compared with the concentrations of CO₂ and CH₄ measured at three distinct experimental sites in the city. The period of study was July 2021. This study also included a comparison between ceilometer data and lidar data, which demonstrated the favorable applicability of the ceilometer data for PBLH estimation. An examination of the correlation between changes in average CO₂ concentrations and PBLH values revealed stronger correlations for the IAG and UNICID stations, with correlation coefficients (ρ) of approximately −0.86 and −0.85, respectively, in contrast to the Pico do Jaraguá station, which exhibited a lower correlation coefficient of −0.42. When assessing changes in CH₄ concentrations against variations in PBL height, the retrieved correlation coefficients were approximately −0.78 for IAG, −0.66 for UNICID, and −0.38 for Pico do Jaraguá. The results indicated that CO₂/CH₄ concentrations are negatively correlated with PBL heights, with CO₂ concentrations showing more significant correlation than CH₄. Additionally, among the three measurement stations, IAG measurements displayed the most substantial correlation. The results from this study contribute to the understanding of the relationship between PBLH and greenhouse gas concentrations, emphasizing the potential of remote sensing systems like ceilometers in monitoring and studying atmospheric processes.