In recent years, YBCO high-temperature superconducting (HTS) tapes have been expected to be applied to devices in power systems or in other industrial applications, owing to their rapidly improving quality and productivity. Our objective is to develop an HTS cyclotron with a compact body, high efficiency of output power, and high performance in heavy particle radiotherapy. In such an application, extremely high precision is required in the range 0.01% to 0.1% of magnetic field, both spatially and temporally. An isochronous field along with an azimuthally varying field is generated by an air-core pancake coil system during construction. Therefore, developing a technology for extremely high coil-winding accuracy is very important. In this study, we constructed an experimental model of a YBCO pancake coil using a high-precision coil winding machine. Then, the winding error in the radial and axial directions was experimentally evaluated using a pair of laser displacement meters and a surface roughness tester. We also developed a numerical simulation model to analyze the influence of winding error on the magnetic field distribution. The relationship between the winding error and the magnetic field of the meter-class YBCO coil assuming a real system was also evaluated by numerical simulation.