With their complex life cycle and highly derived body plan, echinoderms are unique among bilaterians. Although early development has been intensively studied, the molecular mechanisms underlying development of the adult echinoderm and its unusual radial body plan are largely unknown. To investigate the evolution of developmental changes in gene expression underlying radial body plan development and metamorphosis, we assembled a reference transcriptome de novo and used RNA-seq to measure gene expression profiles across larval, metamorphic, and postmetamorphic life cycle phases in the sea urchin Heliocidaris erythrogramma. Our results present a high-resolution view of gene expression dynamics during the complex transition from pre- to postmetamorphic development and suggest that distinct sets of regulatory and effector proteins are used during different life history phases. These analyses provide an important foundation for more detailed analyses of the evolution of the radial adult body of echinoderms.