The unc-51-like kinase protein kinase complex (ULK1C) and the class III phosphatidylinositol (PI) 3-kinase complex I (PI3KC3-C1) are the most upstream and central players in the initiation of macroautophagy in mammals. We found a direct physical interaction between the two complexes. The cryo-EM structures of the human ULK1C core and PI3KC3-C1 were determined at amino acid residue-level resolution, and used to interpret a moderate resolution structure of the ULK1C:PI3KC3-C1 supercomplex. The two complexes co-assemble through extensive contacts between the FIP200 scaffold subunit of ULK1C and the VPS15 pseudokinase subunit of PI3KC3-C1. The presence of PI3KC3-C1 induces a rearrangement of ULK1C from a FIP200:ATG13:ULK1 2:1:1 to a 2:2:2 stoichiometry by dislocating part of the ATG13 intrinsically disordered region (ATG13IDR) from an inhibitory site on the dimeric FIP200 scaffold. This suggests a structural mechanism for the initiation of autophagy through PI3KC3-C1-induced dimerization of ULK1 as bound to FIP200, followed by an activating trans-autophosphorylation of ULK1.