The extinct echinoderm clade Stylophora consists of some of the strangest known deuterostomes. Stylophorans are known from complete, fully articulated skeletal remains from the middle Cambrian to the Pennsylvanian, but remain difficult to interpret. Their bizarre morphology, with a single appendage extending from a main body, has spawned vigorous debate over the phylogenetic significance of stylophorans, which were long considered modified but bona fide echinoderms with a feeding appendage. More recent interpretation of this appendage as a posterior “tail-like” structure has literally turned the animal back to front, leading to consideration of stylophorans as ancestral chordates, or as hemichordate-like, early echinoderms. Until now, the data feeding the debate have been restricted to evaluations of skeletal anatomy. Here, we apply novel elemental mapping technologies to describe, for the first time, soft tissue traces in stylophorans in conjunction with skeletal molds. The single stylophoran appendage contains a longitudinal canal with perpendicular, elongate extensions projecting beyond hinged biserial plates. This pattern of soft tissues compares most favorably with the hydrocoel, including a water vascular canal and tube feet found in all typical echinoderms. Presence of both calcite stereom and now, an apparent water vascular system, supports echinoderm and not hemichordate-like affinities.