A novel, practical observation system for measuring tropospheric carbon dioxide (CO<sub>2</sub>) concentrations using a non-dispersive infrared analyzer carried by a small helium-filled balloon (CO<sub>2</sub> sonde), has been developed for the first time. Onboard calibrations, using CO<sub>2</sub> standard gases, is possible to measure the vertical profiles of atmospheric CO<sub>2</sub> accurately with a 240–400 m altitude resolution. The standard deviations (1σ) of the measured mixing ratios in the laboratory experiments using a vacuum chamber at a temperature of 298 K were approximately 0.6 ppm at 1010 hPa and 1.2 ppm at 250 hPa. Compared with in situ aircraft data, although the difference up to the altitude of 7 km was 0.6 ± 1.2 ppm, this bias and difference were within the precision of the CO<sub>2</sub> sonde. In field experiments, the CO<sub>2</sub> sonde detected an increase in CO<sub>2</sub> concentration in an urban area and a decrease in a forested area near the surface. The CO<sub>2</sub> sonde was shown to be a useful instrument for observing and monitoring the vertical profiles of CO<sub>2</sub> concentration in the troposphere.