Nuclear receptor subfamily 6, group A, member 1 (NR6A1), also known as germ cell nuclear factor/retinoid receptor-related testis-associated receptor and neuronal cell nuclear factor, is a member of the nuclear orphan receptor superfamily. NR6A1 has been cloned in various species including humans and mice, but it has been scarcely investigated in avian species. In the present study, we cloned the chicken NR6A1 (cNR6A1) from a testis cDNA library. The cloned cNR6A1 sequence was mapped to chromosome 17 and contained an open reading frame of 1.4 kb encoding 445 amino acids. Multiple alignment analysis of the cNR6A1 protein-coding sequence with NR6A1s from humans, mice, boars, rats, zebrafish, and Xenopus showed high degrees of homology, 89%, 90%, 89%, 88%, 83%, and 87%, respectively. Using RNA interference, changes in the expression of pluripotency-, germ cell-, and differentiation-related key genes by silencing of cNR6A1 were validated in chicken blastoderm-derived embryonic stem cells. Among those genes, the relative expression levels of POU5F1, CRIPTO, DAZL, DDX4, BMP15, GSC, and SOX7 changed significantly compared to the control group. We also confirmed that the activity of alkaline phosphatase, known as a pluripotency marker, was maintained by cNR6A1 gene silencing in chicken blastodermal cells. Collectively, our data suggest that cNR6A1 may play an important role during chicken embryonic development and differentiation.