Aggregation of α-synuclein (α-syn) into toxic fibrils is a pathogenic hallmark of Parkinson’s disease (PD). This research aimed to develop peptides capable of inhibiting α-syn aggregation using a semi-rational design combined with a multiplexed intracellular Protein-fragment Complementation Assay (PCA) library screening system. Successfully selected peptides must bind to full length α-syn and lower its toxicity to confer bacterial growth. PCA selected peptides were characterized using several biophysical assays and a cell viability assay. The peptides were screened using library templates based on α-syn71-82 initially and later on the α-syn45-54 region in which many key mutations associated with early onset PD are found. In both cases we targeted the peptide libraries at the wild type protein or again by using mutated versions of α-syn. Results demonstrate that some of those selected peptides had the effect of delaying or even preventing the aggregation process, with others providing more subtle effects in reversing the fully formed amyloid fibrils. PCA peptides selected against 71-82 region of wild type α-syn showed a moderate level of efficacy whereas against mutants, it showed a low level of efficacy in inhibiting amyloid fibril formation. In the final part of the study, the peptide selected against 45-54 region of wild type α-syn was capable of preventing the aggregation and reducing the amyloid cytotoxicity at an equimolar ratio. We have thus demonstrated that the PCA strategy can be used as a generalised method for deriving peptide antagonists of α-syn aggregation, together with a new region; α-syn45-54 as an inhibitor target and produced a peptide inhibitor expected to provide a scaffold for future drug candidates to slow or even prevent the onset of PD.