The anteroposterior (A/P) axis is a conserved feature of bilateral animals and is defined in the anterior by a head and in the posterior by a trunk. The secreted family of Wnt proteins and their antagonists play a conserved role in setting up this axis during early development in many bilaterians. The widely accepted model for the role of Wnt signalling in A/P axis specification is by the establishment of a simple activity gradient whereby high levels of Wnt lead to posterior fates and low levels to anterior fates. In this study we further test this model, examining the role of Wnt signaling in the acorn worm, a representative of hemichordates that belongs to the superphylum Deuterostomia along with chordates. We find strong evidence supporting the hypotheses that Wnt signaling represses anterior fates and promotes more caudal fates in the ectoderm, in a similar way to central nervous system development in vertebrates However, we find that the most posterior territory is established independently of Wnt signalling, which is inconsistent with the prevailing model of Wnt function in A/P patterning. We conclude that these data are not inconsistent with vertebrate patterning data and may represent a conserved feature of deuterostome axis patterning.