The onboard atomic frequency standard (AFS) is a crucial element of Global Navigation Satellite System (GNSS) satellites. However, it is widely accepted that periodic variations can influence the onboard AFS. The presence of non-stationary random processes in AFS signals can lead to inaccurate separation of the periodic and stochastic components of satellite AFS clock data when using least squares and Fourier transform methods. In this paper, we characterize the periodic variations of AFS using Allan and Hadamard variances and demonstrate that the Allan and Hadamard variances of the periodics are independent of the variances of the stochastic component. The proposed model is tested against simulated and real clock data, revealing that our approach provides more precise characterization of periodic variations compared to the least squares method. Additionally, we observe that overfitting periodic variations can improve the precision of GPS clock bias prediction, as indicated by a comparison of fitting and prediction errors of satellite clock bias.