Two processes that are key features of Alzheimer’s disease (AD) progression are the aggregation of the peptide amyloid-β (Aβ42) and neuroinflammation. The cytokine S100B is one of the most abundant pro-inflammatory proteins in the brain and is chronically up-regulated in AD. This known biomarker for brain distress is also found to be associated with Aβ42 deposits in AD, and may thus play a role in Aβ42 aggregation. We have discovered a novel role for the neuronal S100B protein as a suppressor of Aβ42 aggregation and toxicity. We have combined biochemical and biophysical approaches with cellular models to show that Aβ42 undergoes a dynamic interaction with S100B within the interfacial dimer cleft. We find that this interaction is calcium-dependent, and possibly involves a conformational switching of disordered Aβ42 into an alpha-helix. Kinetic aggregation assays indicate that S100B interferes with both primary and secondary nucleation processes of Aβ42 fibril formation. Furthermore, S100B protects cells from Aβ42-mediated toxicity, rescuing cell viability and decreasing apoptosis induced by Aβ42 in cell culture models. This novel role of S100B as a direct molecular chaperone of Aβ42 provides a mechanistic link between aggregation and inflammation cascades in AD.