Satellite Navigation Systems (SNS) provide Position, Velocity and Time (PVT) services. The SNS is required to maintain its own System Time with high accuracy. To set up the precise System Time, each system component should maintain its own time within a specified limit. In the SNS, the onboard Space Vehicle (SV) time generator is one of the components and it should be set and maintained with few nanoseconds accuracy. To achieve accurate time setting with minimum difference between the ground and onboard SV systems, the onboard time setting should be highly predictable and accurate. This paper proposes an approach to initialize/set the onboard SV Time. The paper also discusses the concept of synchronization of SV Time with System Time with an overall accuracy better than 1 nsec. The proposed technique requires minimum setting time and synchronization steps and there is no need to predict accurate uplink propagation delay and command execution time.