In this paper we are presenting a methodology, which can remove the effect of ionosphere refraction (ionosphere error) on the coordinates derived by single frequency GPS receivers up to 85 percent at a radius of 1400 km around the computational point. The method is based on the GPS observations being made at the permanent GPS stations, according to the following procedure: (i) The real-time GPS observations being made at the permanent GPS station is compared, epoch-wise, with precisely known coordinates of the permanent station and the time series of coordinate variations in x, y, and z component {∆xi, ∆x, ∆z} is derived. (ii) Fast Fourier technique is applied in order to transfer each components of the variations vector from the time domain into frequency domain. (iii) The plot of the resulted period gram provided us with the frequency vector {fx, fy, fz} of the ionosphere refraction (ionosphere error) with nearly 24 hour period. (iv) Having derived the frequency vector of the ionosphere refraction, a sinusoidal models of the form Sxi =ai0+ai1cos(wit-ψi ) (where w=2πƒ ) is fitted to the coordinate differences {∆x, ∆y, ∆z} via least squares technique. As a case study, 25 day observations of the permanent GPS station of Tehran National Cartographic Center (NCC) is used.