The photochemical thiol-ene reaction is an efficient method for rapid and chemoselective formation of thioether linkages under mild conditions. It has found widespread use in small-molecule synthesis as well as peptide and protein chemistry. While high-throughput experimentation provides an invaluable tool for drug discovery, the considerable potential of the thiol-ene reaction remains unexplored in this context. Herein, we report the development of nanomole-scale photochemical thiol-ene chemistry, performed using an automated approach in 1536-well plates in a cost-efficient custom reactor. Through careful reaction design and selection of reactants, this chemistry is applied to the lateral diversification of peptidic macrocycles to yield high purity crude mixtures. Selection of the photoinitiator 2,2-dimethoxy-2-phenylacetophenone yields volatile breakdown products, which facilitates removal in vacuo. We demonstrate the use of this approach in late-stage diversification of peptidic macrocycles with 96 examples averaging 95% conversion to the desired product.