Since carrier tracking in presence of ionospheric scintillation is non-stationary, nonlinear and non-Gaussian, the conventional discriminator or Kalman filter-based methods used to enhance the robustness of tracking loops are less effective. A carrier tracking algorithm for scintillation mitigation was proposed based on online wavelet denoising, which can characterize the nonstationary scintillation signal much better. By designing a sliding windowbased online wavelet de-noising filer after the integration of I and Q channels, the non-Gaussian noise caused by scintillation can be filtered effectively. As a result, the effect of ionospheric scintillation on loop discriminator is mitigated, and the accuracy and robustness of the tracking loop is improved. Experimental results prove the validity of the analysis and the proposed carrier tracking algorithm.