The evolutionary origin of the vertebrate head remains a focal point in chordate evolutionary developmental biology. Integral to this discussion are the neural crest, placodes, and prechordal plate—key elements believed to be pivotal in the development of the vertebrate head but seemingly absent in amphioxus, a close relative of basal chordates. To shed light on this subject, we employed single-cell transcriptomic analysis to scrutinize embryonic cells from four developmental stages. Utilizing the Seurat pipeline and a diffusion-based computational approach, we revealed the prechordal plate and neural crest-like populations in the developing amphioxus embryo. Our comprehensive analysis establishes regulatory-stage homology in the development of the prechordal plate in chordates and highlights the critical roles of the Nodal and Shh pathways in head formation, similar to their roles in vertebrates. These findings suggest that key features of vertebrate head development may be traced back to the common ancestor of all chordates.