This paper discusses the IEEE 1588 implementation with Frequency Locked Loop (FLL) and Phase Locked Loop (PLL). The work was supported by a Telecom technology provider; the objective is to study the feasibility of IEEE 1588 in the Base Stations (BSs) synchronization, on the basis of minimum structure changes. In order to meet the requirements of the mobile communication systems, IEEE 1588 was implemented using two different methods - the FLL and PLL. Based on the synchronization result, it is observed that the FLL method shows over adjustments when the network Packet Delay Variation (PDV) is large while the PLL method is likely to be affected by the amount of traffic from the master to the slave clock. Additionally, it is also observed that the overdamped PLL gives high frequency accuracy, but also amplifies the effect of PDV, resulting in a larger frequency instability.