Six/sine oculis (Six/so) class genes, with representatives in vertebrates and invertebrates, include members with key developmental roles in the anterior part of the central nervous system (CNS) and eye. Having characterized the role of the first planarian gene of the Six/so family in eye development, we attempted to identify novel genes of this family related to the platyhelminth eye genetic network. We isolated a new Six/so gene in the planarian Girardia tigrina, Gtsix-3, which belongs to the Six3/6 class. Whole mount in situ hybridization revealed Gtsix3 expression in a stripe surrounding the cephalic ganglia in adults. This spatial pattern corresponds to the cephalic branches, the nerve cells that connect the CNS with the marginal sensory organs located continuously at the edge of the head. During head regeneration, Gtsix-3 shows delayed activation compared to other head genes, with an initial two spot pattern that later evolves to a continuous lateral expression in the new regenerated cephalic ganglia with a final reduction to the adult pattern. However, Gtsix-3 is not activated in tail regeneration and no eye expression is observed at any regenerative stage. These findings provide a new marker for the developing anterior nervous system and evidence the complexity of planarian brain.