The safety of a medicinal product is determined by its pharmacological and toxicological profile, which depends not only on the active substance’s toxicological properties, but also on the impurities it contains. Because impurities are a problem that must be considered to ensure the safety of a drug product, many studies have been conducted regarding the separation or purification of active pharmaceutical ingredients (APIs) and the determination of impurities in APIs and drug products. Several studies have applied molecularly imprinted polymers (MIPs) to separate impurities in active ingredients and as adsorbents in the sample preparation process. This review presents the design of MIPs and the methods used to synthesise MIPs to separate impurities in APIs and drug product samples, the application of MIPs to separate impurities, and a view of future studies involving MIPs to remove impurities from pharmaceutical products. Based on a comparison of the bulk and surface-imprinting polymerisation methods, the MIPs produced by the surface-imprinting polymerisation method have a higher adsorption capacity and faster adsorption kinetics than the MIPs produced by the bulk polymerisation method. However, the application of MIPs in the analysis of APIs and drug products are currently only related to organic compounds. Considering the advantages of MIPs to separate impurities, MIPs for other impurities still need to be developed, including multi-template MIPs for simultaneous separation of multiple impurities.