Using polymers for protein encapsulation can enhance stability in processing environments and prolong activity and half-life in vivo. However, finding the best polymer structure for a target protein can be difficult, labour- and cost-intensive. In this study we introduce a high throughput screening approach to identify strong polymer–protein interactions by use of Förster Resonance Energy Transfer (FRET), enabling a rapid read out. We iteratively screened a total of 288 polymers containing varying hydrophilic, hydrophobic, anionic and cationic monomers against a panel of eight different enzymes (glucose oxidase, uricase, manganese peroxidase, bovine serum albumin, carbonic anhydrase, lysozyme, trypsin and casein). By optimisation of the assay conditions it was possible to read out strongly binding polymers at protein concentrations down to 0.1 μM. We were able to use the screening data to locate moderately selective polymer binders in most cases, and elucidate general trends in polymer design that lead to strong binding. Interestingly, these trends are not consistent across proteins, underscoring the value of a screening approach for identification of the best polymers. We applied this technique to identify lead polymers suitable for encapsulation of the important therapeutic protein TNF-related apoptosis-inducing ligand (TRAIL), at a concentration of 0.25 μM (5 μg mL−1). This approach should be valuable in the design of polymers for either selective protein binding, or for universal protein repulsion, particularly where the protein is too expensive to work with at high concentrations and large volumes.