Unc-51-like kinases (ULKs) are the most upstream kinases in the initiation of autophagy, yet the molecular mechanisms underlying their function in this key cellular process are poorly understood.By investigating the guanine nucleotide exchange factor (GEF) DENN domain-containing protein 3 (DENND3) and its substrate, the small GTPase Rab12, we have now discovered a novel mechanism accounting for ULK function in autophagy.We demonstrate that DENND3 plays a positive role in starvation-induced autophagy.Under starvation, ULK directly phosphorylates DENND3 at two sites, upregulating DENND3 GEF activity and activating Rab12.DENND3 phosphorylation mutants fail to rescue defects in starvation-induced Rab12 activation caused by DENND3 knockdown.Through binding to LC3 and associating with LC3-positive autophagosomes, active Rab12 facilitates autophagosome trafficking.Together, our data reveal a novel pathway from starvation-induced ULK signaling through DENND3 to Rab12-mediated membrane trafficking required for autophagy.