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Crop models have suggested high sensitivity of soybean [Glycine max (L.) Merr.] to day length and the resultant extension of the growth period as a concept to overcome yield loss due to climate warming. However, experimental validation of this concept is incomplete. The E3 and E4 loci encode phytochrome A isoforms and enhance sensitivity to day length. Our previous study showed that the dominant E4 allele can mitigate yield loss due to warming. In this study, we similarly tested the hypothesis that the dominant E3 allele can reduce yield loss caused by warming. One of the leading Japanese cultivars Enrei (e3/E4) and near‐isogenic lines (NIL‐e3e4, NIL‐E3e4, and NIL‐E3E4) in the Enrei genetic background were grown at near ambient temperature or either 2.0°C or 4.7°C above ambient temperature in temperature‐gradient chambers (TGCs) in a cool region in Japan. The number of days from sowing to beginning of flowering (R1) decreased with increasing temperature, regardless of genotype. However, increasing temperature extended the period from R1 to beginning of pod filling (R3) and increased pod number per plant and seed yield per plant in all genotypes except NIL‐e3e4. Combined data from the TGC experiment and from field trials across three different latitudes showed that the decreased developmental rate during the R1–R3 period can be attributed to longer days, rather than by supra‐optimal temperatures. We conclude that E3, in addition to E4, could potentially increase seed yield in cool regions under future warming. [ABSTRACT FROM AUTHOR]