Precise timekeeping is at the basis of any Global Navigation Satellite System. In this thesis, after an extensive introduction on time and frequency metrology, some of the basic time-related aspects of navigation systems are discussed, and new ideas and solutions are presented. In the first part of the work, the most relevant innovative contributions are related to the mathematical clock model and to the stability analysis of atomic clocks affected by frequency jumps, as well as to the development of a new averaging algorithm for the generation of a robust time scale from an ensemble of atomic clocks. In the second part, devoted to the role of timekeeping in satellite navigation systems, the innovative contributions are mainly about: a revision of the relativistic corrections; the development and testing of a new composite clock, which could be used as a system time scale for the Galileo system; a study on the impact of the light-shift effect on the timing performance of GPS rubidium clocks; the development of a new recursive clock anomalies detector, as well as a discussion about the possible implementations of a clock anomalies detector and a compensation system for on-board applications.