This study identifies a novel mammalian autophagy factor, Atg13, which forms a stable ~3-MDa protein complex with ULK1 and FIP200. Atg13 localizes to the autophagic isolation membrane and is essential for autophagosome formation. Unlike yeast, the formation of the ULK1–Atg13–FIP200 complex is not altered by nutrient conditions. mTORC1 is incorporated into this complex through ULK1 in a nutrient-dependent manner and phosphorylates ULK1 and Atg13. ULK1 is dephosphorylated by rapamycin treatment or starvation. These findings suggest that mTORC1 suppresses autophagy by directly regulating the ULK1–Atg13–FIP200 complex.This study identifies a novel mammalian autophagy factor, Atg13, which forms a stable ~3-MDa protein complex with ULK1 and FIP200. Atg13 localizes to the autophagic isolation membrane and is essential for autophagosome formation. Unlike yeast, the formation of the ULK1–Atg13–FIP200 complex is not altered by nutrient conditions. mTORC1 is incorporated into this complex through ULK1 in a nutrient-dependent manner and phosphorylates ULK1 and Atg13. ULK1 is dephosphorylated by rapamycin treatment or starvation. These findings suggest that mTORC1 suppresses autophagy by directly regulating the ULK1–Atg13–FIP200 complex.