We contribute to the debate on the identification of phase scintillation induced by the ionosphere on the global navigation satellite system (GNSS) by introducing a phase detrending method able to provide realistic values of the phase scintillation index at high latitude. It is based on the fast iterative filtering signal decomposition technique, which is a recently developed fast implementation of the well-established adaptive local iterative filtering algorithm. FIF has been conceived to decompose nonstationary signals efficiently and provide a discrete set of oscillating functions, each of them having its frequency. It overcomes most of the problems that arise when using traditional time-frequency analysis techniques and relies on a consolidated mathematical basis since its a priori convergence and stability have been proved. By relying on the capability of FIF to efficiently identify the frequencies embedded in the GNSS raw phase, we define a method based on the FIF-derived spectral features to identify the proper cutoff frequency for phase detrending. To test such a method, we analyze the data acquired from GPS and Galileo signals over Antarctica during the September 2017 storm by the ionospheric scintillation monitor receiver (ISMR) located in Concordia Station (75.10° S, 123.33° E). Different cases of diffraction and refraction effects are provided, showing the capability of the method in deriving a more accurate determination of the index. We found values of cutoff frequency in the range of 0.73-0.83 Hz, providing further evidence of the inadequacy of the choice of 0.1 Hz, which is often used when dealing with ionospheric scintillation monitoring at high latitudes.