Wnt/β‐catenin signaling is involved in the formation of the apical ectodermal ridge (AER) during vertebrate limb development. Although Wnt3a is a potent ligand for chick AER formation, whether chick Wnt3a can induce Fgf8 expression in chick embryos is unclear and the Wnt ligand involved in chick AER formation remains unknown. Here, we examined whether another Wnt3a isoform is expressed in the AER, and whether Wnt3 contributes to AER formation in chick as well as mouse embryos. We found that chick Wnt3 was not expressed in the presumptive limb ectoderm at the early stages of AER formation. Using 5′‐rapid amplification of cDNA ends, we isolated another chick Wnt3a transcript. This novel variant, Wnt3a variant 2, induced Fgf8 in the limb ectoderm and activated the β‐catenin pathway in vivo and in vitro. These data showed that Wnt3a variant 2 is an active form of chick Wnt3a that regulates chick AER formation.