Three soybean (Glycine max L. Merr.) cultivars (Maple Glen, Clark and CNS) were exposed to three CO2 concentrations (370, 555 and 740 μmol mol−1) and three growth temperatures (20/15°, 25/20° and 31/26°C, day/night) to determine intraspecific differences in single leaf/whole plant photosynthesis, growth and partitioning, phenology and final biomass. Based on known carboxylation kinetics, a synergistic effect between temperature and CO2 on growth and photosynthesis was predicted since elevated CO2 increases photosynthesis by reducing photorespiration and photorespiration increases with temperature. Increasing CO2 concentrations resulted in a stimulation of single leaf photosynthesis for 40–60 days after emergence (DAE) at 20/15°C in all cultivars and for Maple Glen and CNS at all temperatures. For Clark, however, the onset of flowering at warmer temperatures coincided with the loss of stimulation in single leaf photosynthesis at elevated CO2 concentrations. Despite the season-long stimulation of single leaf photosynthesis, elevated CO2 concentrations did not increase whole plant photosynthesis except at the highest growth temperature in Maple Glen and CNS, and there was no synergistic effect on final biomass. Instead, the stimulatory effect of CO2 on growth was delayed by higher temperatures. Data from this experiment suggest that: (1) intraspecific variation could be used to select for optimum soybean cultivars with future climate change; and (2) the relationship between temperature and CO2 concentration may be expressed differently at the leaf and whole plant levels and may not solely reflect known changes in carboxylation kinetics.