Misfolding of native soluble proteins and peptides into insoluble amyloid aggregates is associated with a number of neurodegenerative disorders, including the most prevalent Alzheimer’s disease and Parkinson’s disease, which generally lead to cognitive decline and motor deficits. Although multiple therapies have made it to clinical trials, to date there are still no clinically effective treatments to cure these diseases or halt their progression. Development of inhibitors that prevent amyloid aggregation and recognize the toxic species to promote their clearance is one of the most important therapeutic strategies. Among different types of inhibitors, peptide-based molecules are promising candidates due to their high specificity, low toxicity, high chemical diversity, proteolytic stability and blood-brain barrier permeability after modification. Here we review the progress in research of peptide-based inhibitors towards the amyloid aggregation of Alzheimer’s disease related Aβ and Tau and Parkinson’s disease related α-synuclein. The peptide inhibitors summarized here have been mainly generated through rational design based on the amyloidogenic sequences and fibril core structures or through random selection from peptide libraries. These peptide molecules, both naturally occurring and synthetic, can inhibit protein aggregation, disassemble amyloid fibrils, reduce cytotoxicity and some have been shown to reduce brain damage and relieve cognitive and motor impairments in animal models. These studies demonstrate the advantages of peptide-inhibitors as anti-amyloid drugs and will facilitate the discovery of new therapeutic agents.