GPS radio occultation can estimate ionospheric electron density and total electron content (TEC) with high spatial resolution, e.g., China's recent Fengyun-3C GPS radio occultation. However, high-order ionospheric delays are normally ignored. In this paper, the high-order ionospheric effects on electron density estimation from the Fengyun-3C GPS radio occultation data are estimated and investigated using the NeQuick2 ionosphere model and the IGRF12 (International Geomagnetic Reference Field, 12th generation) geomagnetic model. Results show that the high-order ionospheric delays have large effects on electron density estimation with up to 800 el cm⁻³, which should be corrected in high-precision ionospheric density estimation and applications. The second-order ionospheric effects are more significant, particularly at 250–300 km, while third-order ionospheric effects are much smaller. Furthermore, the high-order ionospheric effects are related to the location, the local time, the radio occultation azimuth and the solar activity. The large high-order ionospheric effects are found in the low-latitude area and in the daytime as well as during strong solar activities. The second-order ionospheric effects have a maximum positive value when the radio occultation azimuth is around 0–20°, and a maximum negative value when the radio occultation azimuth is around −180 to −160°. Moreover, the geomagnetic storm also affects the high-order ionospheric delay, which should be carefully corrected.