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This paper presents a study of phase synchronization impact on throughput in Long Term Evolution (LTE) network with different transport protocols. Phase synchronization is needed for advanced features in LTE and other precise technologies with minimal clock error of Nano seconds. An End to End LTE testing environment is built by using real User Equipment (UE) and LTE core network for studying the throughput impact due to Phase Synchronization in different transport modes. This experimentation is carried out for comparing the throughput of the system with Frequency Synchronization Mode (FM) and Frequency & Phase synchronization Mode (FPM). A novel study has been conducted on throughput for TCP and UDP traffic in different LTE bandwidths, based on real traffic conditions. The study shows that system performance in Uplink (UL) and Downlink (DL) throughput has improved by using Frequency along with Phase synchronization in LTE network using GPS as a clock source.