Understanding the effects of climate change is vital for food security. Among the most important environmental impacts of climate change is the direct effect of increased atmospheric carbon dioxide concentration ([CO2]) on crop yields, known as the CO2 fertilization effect. Although several statistical studies have estimated past impacts of temperature and precipitation on crop yield at regional scales, the impact of past CO2 fertilization is not well known. We evaluated how soybean yields have been enhanced by historical atmospheric [CO2] increases in three major soybean-producing countries. The estimated average yields during 2002-2006 in the USA, Brazil, and China were 4.34%, 7.57%, and 5.10% larger, respectively, than the average yields estimated using the atmospheric [CO2] of 1980. Our results demonstrate the importance of considering atmospheric [CO2] increases in evaluations of the past effects of climate change on crop yields.