In the colonial ascidian Botryllus schlosseri, long-lived germline stem cells (GSCs) migrate to new germline niches as they develop during repetitive cycles of asexual reproduction. ABC-transporters are involved in the export of lipid-signaling molecules, but their roles in germ cell migration are poorly understood. Here, we show that in Botryllus, abcc1 and abcb1 are highly expressed in germ cells, and inhibition of ABCtransporter activity leads to failure of germ cell migration. Phospholipase A2 (PLA2) produces arachidonic acid, which is further metabolized to eicosanoid signaling molecules. In humans, 12-lipoxygenase (LOX) metabolizes arachidonic acid to12-Hydroxyeicosatetraenoic acid (12-S-HETE), which stimulates migration of mammalian cancer cells and smooth muscle cells. We show that PLA2 and LOX activity are required for germ cell migration. A potential homolog to the human receptor for 12-S-HETE, BSgpr31, is expressed in germ cells. 12-S-HETE rescues migration towards S1P in the presence of inhibitors of ABCC1, ABCB1, PLA2 or LOX, and a gradient of 12-S-HETE enhances chemotaxis towards S1P and stimulates motility. We conclude that 12-S-HETE is a secondary chemoattractant exported by ACB-transporters that is required for migration of germ cells towards S1P. We also find that in the presence of S1P, detection of an 12-S-HETE gradient initiates an autologous positive feedback loop that may sustain migration. This is the first report of an eicosanoid-signaling molecule regulating germ cell migration.