The epithelial to mesenchymal transition (EMT) is a highly conserved morphogenetic program essential for embryogenesis, regeneration and cancer metastasis. In cancer cells, EMT also triggers cellular reprogramming and chemoresistance, which underlie disease relapse and decreased survival. Hence, identifying compounds that block EMT is essential to prevent or eradicate disseminated tumor cells. Here, we establish a whole animal-based EMT reporter in zebrafish for rapid drug screening called Tg(snai1b:GFP), which labels epithelial cells undergoing EMT to produce sox10-positive neural crest (NC) cells. Time-lapse and lineage analysis of Tg(snai1b:GFP) embryos reveal that cranial NC cells delaminate from two regions; an early population delaminates adjacent to the neural plate while a later population delaminates from within the dorsal neural tube. Treating Tg(snai1b:GFP) embryos with candidate small molecule EMT compounds identified TP-0903, a multi-kinase inhibitor that blocked cranial NC delamination in both the lateral and medial populations. RNA-Seq analysis and chemical rescue experiments show TP-0903 acts through stimulating retinoic acid (RA) biosynthesis and RA-dependent transcription. These studies identify TP-0903 as a new therapeutic for activating RA in vivo and raise the possibility that RA-dependent inhibition of EMT may contribute to its prior success in eliminating disseminated cancer cells.