To mitigate these effects, an adaptive signal decomposition technique called Variational Mode Decomposition (VMD), combined with Detrended Fluctuation Analysis (DFA), is proposed. VMD-DFA effectively decomposes the GNSS signal affected by scintillations into intrinsic mode functions, providing a threshold for detecting and mitigating scintillation noise. Monte Carlo simulations show that the proposed algorithm outperforms the complementary Ensemble Empirical Mode Decomposition method in eliminating amplitude scintillation effects. The algorithm's efficacy is demonstrated on both synthetic (Cornell scintillation model) and real-time measured GNSS data from Rio de Janeiro, Brazil, indicating its potential in mitigating ionospheric amplitude scintillation effects.