This paper presents a IEEE1588 based clock synchronization technique for a sRIO (Serial RapidIO) network which is applied to a submarine system. Clock synchronization plays a key role in the success of a networked embedded system. Recently, the IEEE1588 algorithm making use of dedicated chipset has been widely used for the synchronization of various industrial applications. However, there is no chipset available for the sRIO network that can offer many advantages, such as low latency and jitter. In this paper, the IEEE1588 algorithm for a sRIO network is implemented using only software without any dedicated chipset. The proposed approach is verified with experimental setup.