Regeneration involves the integration of new and old tissues in the context of an adult life history. It is clear that the core conserved signaling pathways that orchestrate development also play central roles in regeneration and further study of conserved signaling pathway is required. Here we have studied the role of the conserved JNK signaling cascade during planarian regeneration. Abrogation of JNK signaling by RNAi or pharmacological inhibition blocks posterior regeneration and animals fail to express posterior markers. While early injury induced expression of polarity markers is unaffected, the later stem cell dependent phase of posterior Wnt expression is not established. This defect can be rescued by over-activation of the Hh or Wnt signaling pathway to promote posterior Wnt activity. Together our data suggest JNK signaling is required to establish stem cell dependent Wnt expression after posterior injury. Given that in vertebrates Jun has been previously shown to be required for the expression of Wnt and Wnt target genes, we propose that this interaction may be conserved and is an instructive part of planarian posterior regeneration.