Ionospheric scintillation effects degrade satellite-based radio communication/navigation links and influence the performance of Global Navigation Satellite Systems (GNSS). An adaptive wavelet-based decomposition technique, Synchrosqueezing Transform (SST), with a Detrended Fluctuation Analysis (DFA) algorithm has been implemented for time-frequency representation of GNSS multi-component signals and mitigation of scintillation effects. Synthetic In-phase (I) and Quadra-phase (Q) samples were collected from the Cornell Scintillation Model (CSM) and the CSM amplitude scintillation signal was processed with SST-DFA for the detection of noisy scintillation components and mitigation of ionospheric scintillation effects. Also, performance of the SST-DFA algorithm was tested for real-time GNSS ionospheric scintillation data collected from a GNSS Software Navigation Receiver (GSNRx) located at a low-latitude station in Rio de Janeiro, Brazil. The de-noising performance of the SST-DFA algorithm was further evaluated and compared with a low-pass Butterworth filter during different ionospheric scintillation time periods. The experimental results clearly demonstrated that the proposed method is reliable for mitigation of ionospheric scintillation noise both in time and frequency scales.