As switchgrass (Panicum virgatum L.) and high biomass sorghum (Sorghum bicolor L. Moench) acreages are expanding for cellulosic biofuels, it is critical to improve understanding of carbon dynamics of these two potential bioenergy crops. Eddy flux measurements from co-located switchgrass and high biomass sorghum fields during the 2012 and 2013 growing seasons were analyzed to quantify and compare net ecosystem CO2 exchange (NEE) between two species. Monthly ensemble averaged NEE reached seasonal peak values of −36.9 ± 1.78 and −35.9 ± 2.32 μmol m−2 s−1 in switchgrass and sorghum, respectively. Similar magnitudes of NEE (−10 to −11 g C m−2 d−1), gross primary production (GPP, 19–20 g C m−2 d−1) and ecosystem respiration (ER, 10–12 g C m−2 d−1) were observed in both ecosystems. Similarly, carbon fluxes of both ecosystems had similar response to air temperature and vapor pressure deficit (VPD). Carbon fluxes exhibited an optimum temperature of slightly over 30 °C and decreased markedly beyond 35 °C. The NEE decreased markedly at higher VPD (>3 kPa) because of the stomatal closure control of photosynthesis. The switchgrass field was a larger carbon sink, with a cumulative seasonal carbon uptake of −406 ± 24 to −490 ± 59 g C m−2 compared to −261 ± 48 to −330 ± 45 g C m−2 by the sorghum field. The switchgrass stand was a net carbon sink for four to five months (April/May–August), while sorghum appeared to be a net carbon sink for only three months (June–August). Our results imply that the difference in carbon sink strength between the two species was driven mainly by the length of the growing season.