The major maturity gene E1 has the most prominent effect on flowering time and photoperiod sensitivity of soybean, but the pathway mediated by E1 is largely unknown. Here, we found the expression of GmFT4, a homolog of Flowering Locus T, was strongly up-regulated in transgenic soybean overexpressing E1, whereas expression of flowering activators, GmFT2a and GmFT5a, was suppressed. GmFT4 expression was strongly up-regulated by long days exhibiting a diurnal rhythm, but down-regulated by short days. Notably, the basal expression level of GmFT4 was elevated when transferred to continous light, whereas repressed when transferred to continuous dark. GmFT4 was primarily expressed in fully expanded leaves. Transcript abundance of GmFT4 was significantly correlated with that of functional E1, as well as flowering time phenotype in different cultivars. Overexpression of GmFT4 delayed the flowering time in transgenic Arabidopsis. Taken together, we propose that GmFT4 acts downstream of E1 and functions as a flowering repressor, and the balance of two antagonistic factors (GmFT4 vs GmFT2a/5a) determines the flowering time of soybean.