In all metazoans, early embryogenesis is driven by maternal RNAs until zygotic transcription begins several hours later. During this maternal-to-zygotic transition (MZT), mRNA translation and stability regulation is essential. Thus, early embryogenesis is governed entirely by RNA biology; yet the RNA-binding proteins (RBPs) that interact with RNA are largely unknown. Here we identify 223 mRNA-bound proteins (mRBPs) in zebrafish embryos before and during zygotic transcriptional onset, including a subset of stage- and species-specific mRBPs. We show that hnRNP A1, an abundant component of the interactome, exhibits unusual 3’UTR binding. This is surprising, because hnRNPs bind mostly to introns in somatic cells. Furthermore, hnRNP A1 associated with zygotic m6A modified pri-miR430 transcripts, implicating hnRNP A1 in the biogenesis of miR430, which is essential for maternal mRNA degradation during MZT. Our study uncovers core regulators of embryonic RNA and suggests that hnRNP proteins adopt unconventional RNA processing roles to promote vertebrate development.