Cardiac valve disease is a common cause of congenital heart failure. Cardiac valve development requires a complex regulation of assorted protease activities. Nevertheless, the regulation of these proteases during atrioventricular (AV) valve formation is poorly understood. Previously, PRSS23, a novel vascular protease, is shown to be highly expressed at the AV canal during murine heart development; however, its function remains unknown. In this study, we sought to characterize the functional role of PRSS23 during cardiac valve formation. We used a transgenic zebrafish line with fluorescently labelled vasculature as a tool to study the function of PRSS23. We first cloned the zebrafish prss23 and confirmed its sequence conservation with other vertebrate orthologues. Expression of prss23 was detected in the ventricle, atrium, and AV canal during zebrafish embryonic development. We found that morpholino knockdown of Prss23 inhibited the endothelial-to-mesenchymal transition (EndoMT) at the AV canal. Moreover, in human aortic endothelial cell-based assays, PRSS23 knockdown by short-hairpin RNA not only repressed the transforming growth factor-β-induced EndoMT, but also reduced Snail transcription, suggesting that Snail signalling is downstream of PRSS23 during EndoMT. We further demonstrated that human PRSS23 and SNAIL could rescue the prss23 morpholino-induced AV canal defect in zebrafish embryos, indicating that the function of PRSS23 in valvulogenesis is evolutionarily conserved. We demonstrated for the first time that the initiation of EndoMT in valvulogenesis depends on PRSS23-Snail signalling and that the functional role of PRSS23 during AV valve formation is evolutionarily conserved.