The projected increase of atmospheric CO2 concentration ([CO2]) is expected to increase rice yield, but little is known of the effects of [CO2] at low temperature, which is the major constraint to growing rice in cool climates. We grew rice under two levels of [CO2] (ambient and elevated by 200 μmol mol−1) and two nitrogen (N) fertilization regimes in northern Japan in 2003 (cool weather) and 2004 (warm weather) in the field in a free-air CO2 enrichment (FACE) system. Elevated [CO2] significantly increased grain yield in both years in both N regimes, but the magnitude of the increase differed between years: 6% in 2003 vs. 17% in 2004, with a significant interaction between [CO2] and year. This difference resulted from responses of spikelet number and ripening percentage to elevated [CO2]. Enhancement of dry matter production and N uptake at heading by elevated [CO2] was smaller in 2003 than in 2004, although at maturity there was no difference between years. No significant interaction between N regime and [CO2] was detected in yield and yield components. The results suggest that yield gain due to elevated [CO2] can be reduced by low temperature.