Despite intense interest in the proteolysis of Amyloid Precursor Protein (APP) in Alzheimer’s disease (AD), how the normal processing and function of this type I receptor-like glycoprotein is regulated remains ill-defined. APP is reported to function in neurodevelopment, including migration of neuronal precursor cells into the cortical plate. In recent years, several candidate ligands for APP, including F-spondin, Reelin, \(\beta1\) Integrin, Contactins, and Lingo-1 have been reported. However, a cognate ligand for APP that regulates its function or processing has yet to be widely confirmed in multiple laboratories. First, in an unbiased approach to reveal novel ligands, Pancortin was identified by a mass spectrometry-based screen for factors that bind to the APP ectodomain in rodent brain. Each of the Pancortin isoforms was confirmed to interact with APP. However, only specific Pancortin isoforms reduced \(\beta\)-secretase but not \(\alpha\)-secretase cleavage of endogenous APP. Using in utero electroporation to overexpress or knockdown Pancortin isoforms in rodent cortex, a previously unidentified role for Pancortin in cortical cell migration with evidence for a functional interaction with APP was discovered. Next, I developed new assays in an effort to confirm a role for one or more of the published candidate ligands in regulating APP ectodomain shedding in a biologically relevant context. A comprehensive quantification of APPs\(\alpha\) and APPs\(\beta\), the immediate products of secretase processing, in both non-neuronal cell lines and primary neuronal cultures expressing endogenous APP yielded no evidence that any of these published candidate ligands stimulate ectodomain shedding. Rather, Reelin, Lingo-1 and Pancortin emerged as the most consistent ligands for significantly inhibiting ectodomain shedding. These studies clarify mechanisms regulating the function and processing of APP, which is needed to understand consequences of chronically altering APP proteolysis to treat AD and to develop new potential drug targets.