The dysregulation of autophagy promotes the development of several diseases like neurodegeneration, infection, or cancer. To keep up with their metabolic demand under low nutrient and/or oxygen conditions typically present in the tumor microenvironment, cancer cells can upregulate autophagy autonomously or in surrounding cells. Therefore, the inhibition of autophagy is desired in these settings. However, to date drugs selectively targeting autophagy remain rare. The autophagy-inducing ULK1 complex comprises ULK1/2, FIP200 and a heterodimer consisting of ATG13 and ATG101. Our group previously described that the ATG13-ATG101 protein-protein interaction (PPI) is essential for both the assembly of the ULK1 complex and cellular autophagic activity. Here, we describe the identification of four compounds selectively inhibiting autophagy by targeting this PPI. The compounds were identified either by a homogeneous time-resolved fluorescence (HTRF)-based screening with a library of 15,488 compounds or by virtual screening on the commercially available part of the ZINC20 library and a section of the MolPort library. Bimolecular fluorescence complementation (BiFC) was used for the detection of compound-induced interference with the cellular ATG13-ATG101 interaction. The effect on cellular autophagy was investigated by several assays, and the compounds were biophysically characterized using molecular dynamics simulations, spectral shift assays, and STD-NMR. Finally, we observed that the compounds are sensitizing different cancer cell lines to nutrient stress. We propose that these four compounds are promising lead compounds for the development of PPI inhibitors selectively inhibiting the ATG13-ATG101 interaction and thus autophagy.