The misfolding and aggregation of beta-amyloid (A beta) peptides have been implicated as key pathogenic events in the early stages of Alzheimer's disease (AD). Inhibiting A beta aggregation represents a potential disease-modifying therapeutic approach to AD treatment. Previous studies have identified various molecules that inhibit A beta aggregation, some of which share common chemical substructures (fragments) that may be key to their inhibitory activity. Employing fragment-based drug discovery (FBDD) methods may facilitate the identification of these fragments, which can subsequently be used to screen new inhibitors and provide leads for further drug development. In this study, we used an in silico FBDD approach to identify 17 fragment clusters that are significantly enriched among A beta aggregation inhibitors. These fragments were then used to screen anti-infective agents, a promising drug class for repurposing against amyloid aggregation. This screening process identified 16 anti-infective drugs, 5 of which were chosen for further investigation. Among the 5 candidates, anidulafungin, an antifungal compound, showed high efficacy in inhibiting A beta aggregation in vitro. Kinetic analysis revealed that anidulafungin selectively blocks the primary nucleation step of A beta aggregation, substantially delaying A beta fibril formation. Cell viability assays demonstrated that anidulafungin can reduce the toxicity of oligomeric A beta on BV2 microglia cells. Molecular docking simulations predicted that anidulafungin interacted with various A beta species, including monomers, oligomers, and fibrils, potentially explaining its activity against A beta aggregation and toxicity. This study suggests that anidulafungin is a potential drug to be repurposed for AD, and FBDD is a promising approach for discovering drugs to combat A beta aggregation.