Atmospheric CO2 concentrations ([CO2]) have increased by more than 100 μmol mol−1 over the last century and are projected to rise further. Breeding cultivars with a greater response to elevated [CO2] (E-[CO2]) can be an effective adaptation to global climate change. We wondered whether E-[CO2]-responsive cultivars have been unintentionally selected through empirical breeding as [CO2] has increased. If so, modern cultivars may respond better to E-[CO2] than old ones. We conducted free-air CO2 enrichment (FACE) experiments in 2 years to examine whether rice cultivars bred in different eras differ in response to E-[CO2] and to determine any associated traits. We tested five Japanese cultivars: Aikoku (released in 1882), Norin 8 (1934), Koshihikari (1956), Akihikari (1976) and Akidawara (2009). The yields of Aikoku and Norin 8 increased by 19.3% and 30.3%, respectively, under E-[CO2], while those of Koshihikari and Akihikari increased by 15.9% and 3.4%, respectively. However, that of Akidawara, the newest cultivar, also increased by 19.0%. Norin 8’s strong response to E-[CO2] was associated with increases in both spikelet density and percentage of ripened grains, both of which were closely related to nitrogen uptake. These results suggest that breeding has not necessarily improved cultivars’ response to E-[CO2], and that selection for traits such as sink capacity and nitrogen uptake can be effective to improve rice productivity under E-[CO2].