Severe scintillations degrade the satellite signal intensity below the fade margin of satellite receivers thereby resulting in failure of communication, positioning, and navigational services. The performance of satellite receivers is obviously restricted by ionospheric scintillation effects, which may lead to signal degradation primarily due to the refraction, reflection, and scattering of radio signals. Thus, there is a need to develop an ionospheric scintillation detection and mitigation technique for robust satellite signal receivers. Hence, variational mode decomposition (VMD) is proposed. VMD addresses the problem of ionospheric scintillation effects on global navigation satellite system (GNSS) signals by extracting the noise from the radio signals in combination with multifractal detrended fluctuation analysis (MFDFA). MFDFA helps as a criterion designed to detect and distinguish the intrinsic mode functions (IMFs) into noisy (scintillated) and noise-free (non-scintillated) IMF signal components using the MFDFA threshold. The results of the proposed method are promising, reliable, and have the potential to mitigate ionospheric scintillation effects on both the synthetic (simulated) and real GNSS data obtained from Manado station (latitude 1.34° S and longitude 124.82° E), Indonesia. From the results, the effectiveness of VMD-MFDFA over complementary ensemble empirical mode decomposition with MFDFA (CEEMD-MFDFA) is an indication of better performance.