Printed circuit boards (PCBs) are representative composite materials, and their high-quality drilling machining remains a persistent challenge in the industry. The finishing of the cutting edge of a microdrill is crucial to drill performance in machining fine-quality holes with a prolonged tool life. The miniature size involving submicron scale geometric dimensions, a complex flute shape, and low fracture toughness makes the cutting edge of microdrills susceptible to breakage and has been the primary limiting factor in edge preparation for microdrills. In this study, a newly developed cutting edge preparation method for microdrills was tested experimentally on electronic printed circuit boards. The proposed method, namely, shear thickening polishing, limited the cutting edge burrs and chipping on the cutting edge, and this in turn transformed the cutting edge’s radius from being sharp to smooth. Moreover, the edge–edge radius could be regulated by adjusting the processing time. PCB drilling experiments were conducted to investigate the influence of different cutting edge radii on wear, hole position accuracy, nail head value, and hole wall roughness. The proposed approach showed 20% enhancement in hole position accuracy, 33% reduction in the nail head value, and 19% reduction in hole wall roughness compared with the original microdrill. However, a threshold is needed; without it, excessive shear thickening polishing will result in a blunt edge, which may accelerate the wear of the microdrill. Wear was identified as the primary factor that reduced hole quality. The study indicates that in printed circuit board machining, microdrills should effectively eliminate grinding defects and maintain the sharpness of the cutting edge as much as possible to obtain excellent drilling quality. Overall, shear thickening polishing is a promising method for cutting edge preparation of microdrills. Further research and optimization can lead to additional improvements in microdrill performance and contribute to the continued advancement of printed circuit board manufacturing.