Code pseudorange measurements of the Chinese GNSS BeiDou reveal variations which result in code–phase divergences of more than 1 m. We have analyzed these delay variations based on observation data of the International GNSS Service and its Multi-GNSS Experiment campaign. Our results confirm that these code variations are elevation-dependent when observed by receiving antennas on the earth’s surface. In addition, we found significant differences between two groups of satellites and among carrier frequencies. These delay variations have only little effects on absolute BeiDou positioning using broadcast ephemerides due to the limited accuracy of the obtainable positions. But, all precise applications which use code measurements are severely affected. These applications include, e.g., certain algorithms used in Precise Point Positioning (PPP), especially PPP ambiguity fixing and single-frequency PPP based on the ionosphere-free code–carrier combination. We developed a correction model and determined correction parameters in order to accommodate these symptoms. Application examples demonstrate the successful mitigation of these code pseudorange variations.