The red sea urchin, Mesocentrotus franciscanus, is an ecologically important kelp forest species that also serves as a valuable fisheries resource. In this study, we have assembled and annotated a developmental transcriptome for M. franciscanus that represents eggs and six stages of early development (8- to 16-cell, morula, hatched blastula, early gastrula, prism and early pluteus). Characterization of the transcriptome revealed distinct patterns of gene expression that were separated by major developmental and morphological processes. The period during which maternally-controlled transcription was terminated and the zygotic genome was activated, known as the maternal-to-zygotic transition (MZT), was found to begin during early cleavage and persist through the hatched blastula stage, an observation which is similar to the timing of the MZT in other sea urchin species. The presented developmental transcriptome will serve as a useful resource for investigating, within both an ecological and fisheries context, how the early developmental stages of this species respond to stress.