Germ cells are essential to sexual reproduction. Across the animal kingdom, extracellular isoprenoids, such as retinoic acids (RAs) in vertebrates and juvenile hormones (JHs) in insects, impact the germline lifecycle from meiosis to gametogenesis. Emerging evidence suggests that these bioactive isoprenoids also influence embryonic reproductive development, though the precise functions remain unclear. Here, we investigated the specific molecular pathways by which JHs regulates embryonic germ cell development in Drosophila. With a newly generated in vivo reporter, we find that JH signaling is active in the vicinity of germ cells as they migrate to colonize the somatic gonad. Through a combination of in vivo and in vitro assays, we find that JHs are both necessary and sufficient for primordial germ cell migration through mechanisms independent of canonical nuclear receptor-mediated transcription. These findings reveal that JH is present during Drosophila embryogenesis and that bioactive isoprenoids impact germ cell development earlier than previously appreciated. Interestingly, we find that like JH in Drosophila, RA is sufficient for murine germ cell migration in vitro, suggesting that the impact of bioactive isoprenoids on embryonic germ cell development may be broadly conserved.