Net ecosystem CO2 exchange (NEE) was measured in maize-based agroecosystems in eastern Nebraska, USA, during the growing season in 2001. The objective of this study was to quantify and contrast NEE in irrigated and rainfed maize (Zea maize L.) fields. Daytime NEE showed a strong dependence on incident light at different stages of crop growth. Weekly ensemble averaged CO2 flux at the irrigated and rainfed sites reached seasonal peak values of 2.5 and 2.1 mg CO2 m−2 s−1, respectively, occurring when the green leaf area index (LAI) was at its seasonal maximum (6.3 and 4.1 m2 m−2, respectively; planting density was 25% lower at the rainfed site). A dry period during mid-July to mid-August induced moisture stress and caused NEE and LAI to decrease at the rainfed site while values at the irrigated site remained steady. On a seasonal basis, the daytime NEE (at a given value of photosynthetically active radiation (PAR)) and LAI followed the same hyperbolic relationship at the irrigated and rainfed sites, even during periods of soil moisture stress. Nighttime NEE at both sites showed strong dependence on soil temperature. Nighttime NEE (at a given soil temperature) during the later vegetative/reproductive growth stages was higher than the values in the earlier part of the growing season, perhaps due to the relative influence of growth and maintenance respiration. Nighttime NEE at the rainfed site was significantly smaller during periods of moisture stress. Daily gross primary productivity (GPP) reached seasonal peaks of 26 and 24 g C m−2 per day at the irrigated and rainfed sites, respectively. Hourly ensemble averages of GPP were comparable to results from a previous study in rainfed maize and about 1.5–2 times higher than those in soybean, wheat, and in temperate, coniferous, and deciduous forests. Seasonal distributions of the daily gain of carbon by the crop, calculated from measured NEE and estimated soil microbial CO2 flux, compared reasonably well (2–21%) with the total (above and belowground) biomass, given the difficulties involved in such an analysis.