Multilayered polymeric balloon catheters, one of the most important components during interventional treatment, are drawing more attention recently due to the microscale cross section, excellent mechanical properties, and high accuracy. During multilayered polymeric balloon catheter processing, many operating conditions can affect the size and shape of cross sections. In this study, polymer melt flow behavior inside extrusion die is theoretically analyzed first. Then, ethylene vinyl acetate (EVA) and polypropylene (PP) are selected as the build materials to produce the middle and inner layers of three-layered polymeric balloon catheters, while polyamide (PA) and thermoplastic elastomer (TPE) are used to make the outer layer of two types of catheters, respectively. Based on the material selection, a three-layered coaxial die is designed and manufactured to coextrude three different polymer melts to form corresponding catheters. In addition, the effects of operating conditions including outer layer materials, pulling speed, gas flow rate, and screw rotation speeds on the diameters and wall thicknesses as well as the concentricity and ovality of the extrudates are investigated. Finally, the PA-EVA-PP and TPE-EVA-PP three-layered catheters are successfully fabricated, which have well-defined geometries and high shape accuracy.