This study proposes a unified uncombined model to estimate GPS satellite inter-frequency clock bias (IFCB) in both triple-frequency code and carrier-phase observations. In the proposed model, the formulae of both phase-based and code-based IFCBs are rigorously derived. Specifically, satellite phase-based IFCB refers to its time-variant part and it is modeled as a periodic function related to the sun–spacecraft–earth angle. A zero-mean condition of all available GPS satellites that support triple-frequency data is introduced to render satellite code-based IFCB estimable. Three months of data from 40 globally distributed stations of the International GNSS Service Multi-GNSS Experiment are used to test our method. The results show that the four-order periodic function is suitable for eliminating the 12-h, 6-h, 4-h, and 3-h periods that exist in the a posteriori phase residuals when no periodic function is used. For comparison, the geometry-free and ionosphere-free (GFIF) phase combination and differential code bias (DCB) products released by DLR (German Aerospace Center) and IGG (Institute of Geodesy and Geophysics, China) are also used to calculate the satellite phase-based and code-based IFCBs, respectively. The results show that (1) the average root mean square (RMS) of the phase-based IFCB difference between the proposed method and the GFIF phase combination is 4.3 mm; (2) the average RMS in the eclipse period increased by 50% compared with the average RMS in the eclipse-free period; (3) the mean monthly STD for code-based IFCB from the proposed method is 0.09 ns; and (4) the average RMS values of code-based IFCB differences between the proposed method and the DCB products released by DLR and IGG are 0.32 and 0.38 ns. This proposed model also provides a general approach for multi-frequency GNSS applications such as precise orbit and clock determination.