The highly conserved (yeast to human) TSC-mTOR signalling pathway controls central metabolic pathways, including regulating cell growth. Formed by TSC1, TSC2, and TBC1 domain family member 7 (TBC1D7), the TSC is a 700 kDa GTPase-activating protein complex (GAP). TSC deactivates the small GTPase Rheb by catalysing its conversion from the GTP-bound active state to the inactive GDP-bound state. Rheb, in its active GTP-bound state, is required to activate mTORC1 at the lysosomal membrane. Mutation of TSC1 or TSC2 genes can result in the autosomal dominant genetic disorder TSC (also termed tuberous sclerosis), affecting approximately 2 million people worldwide. Here, we use cryo-EM and crosslinking mass spectrometry (XLMS) to investigate the structural basis of TSC docking at the lysosomal membrane. We determine the structure of TSC in complex with WIPI3 and report several high-resolution structural insights into TSC endolysosomal docking. These studies build a detailed picture of TSC docking at the endolysosomal membrane.