Vertical profiles of carbon dioxide (CO2) were captured in rural Ontario, Canada, using an Aeroqual Series 500 monitor mounted onboard an Uncrewed Aerial Vehicle (UAV). Measurements at various altitudes within the Transport Canada regulations height limit (5m – 95m) were compared to simultaneous measurements taken by an identical sensor at ground-level. Results demonstrate a high degree of agreement between onboard and ground-level observations, with a mean different of -6.02 ppm, and the majority of differences falling within the sensor’s factory calibration accuracy (±10 ppm + 5%). The study also demonstrates the ability to capture the homogeneity of CO2 in the lower troposphere, with Intraclass Correlation Coefficients (ICC) exceeding 0.75 at all altitudes, without the addition of turbulence by UAV flight. The vertical profiles captured in this study validate the use of UAV-based measurements for understanding the distribution and transport of greenhouse gases near the surface of the Earth. This research has implications for routine air quality monitoring to improve atmospheric models, environmental impact assessments and the development of targeted emission reduction strategies.