The pharyngeal pouches are a series of epithelial outgrowths of the foregut endoderm. Pharyngeal pouches segment precursors of the vertebrate face into pharyngeal arches and pattern the facial skeleton. These pouches fail to develop normally in zebrafish foxi1 mutants, yet the role Foxi1 plays in pouch development remains to be determined. Here we show that ectodermal Foxi1 acts downstream of Fgf8a during the late stage of pouch development to promote rearrangement of pouch-forming cells into bilayers. During this phase, foxi1 and wnt4a are coexpressed in the facial ectoderm and their expression is expanded in fgf8a mutants. foxi1 expression is unaffected in wnt4a mutants; conversely, ectodermal wnt4a expression is abolished in foxi1 mutants. Consistent with this, foxi1 mutant pouch and facial skeletal defects resemble those of wnt4a mutants. These findings suggest that ectodermal Foxi1 mediates late-stage pouch morphogenesis through wnt4a expression. We therefore propose that Fox1 activation of Wnt4a in the ectoderm signals the epithelial stabilization of pouch-forming cells during late-stage of pouch morphogenesis.