Measurement of carbon dynamics of soybean (Glycine max L.) ecosystems outside Corn Belt of the United States (U.S.) is lacking. This study examines the seasonal variability of net ecosystem CO2 exchange (NEE) and its components (gross primary production, GPP and ecosystem respiration, ER), and relevant controlling environmental factors between rainfed (El Reno, Oklahoma) and irrigated (Stoneville, Mississippi) soybean fields in the southern U.S. during the 2016 growing season. Grain yield was about 1.6tha−1 for rainfed soybean and 4.9tha−1 for irrigated soybean. The magnitudes of diurnal NEE (~2-weeks average) reached seasonal peak values of −23.18 and −34.78μmolm−2s−1 in rainfed and irrigated soybean, respectively, approximately two months after planting (i.e., during peak growth). Similar thresholds of air temperature (Ta, slightly over 30°C) and vapor pressure deficit (VPD, ~2.5kPa) for NEE were observed at both sites. Daily (7-day average) NEE, GPP, and ER reached seasonal peak values of −4.55, 13.54, and 9.95gCm−2d−1 in rainfed soybean and −7.48, 18.13, and 14.93gCm−2d−1 in irrigated soybean, respectively. The growing season (DOY 132–243) NEE, GPP, and ER totals were −54, 783, and 729gCm−2, respectively, in rainfed soybean. Similarly, cumulative NEE, GPP, and ER totals for DOY 163–256 (flux measurement was initiated on DOY 163, missing first 45days after planting) were −291, 1239, and 948gCm−2, respectively, in irrigated soybean. Rainfed soybean was a net carbon sink for only two months, while irrigated soybean appeared to be a net carbon sink for about three months. However, grain yield and the magnitudes and seasonal sums of CO2 fluxes for irrigated soybean in this study were comparable to those for soybean in the U.S. Corn Belt, but they were lower for rainfed soybean.