Wireless Sensor Network (WSN) is a self-configuring and highly flexible distributed network used for real time monitoring and is comprised of a number of wireless, minute, battery-operated independent sensor nodes connected to a common sink. Due to energy considerations, the network is generally divided into clusters and the entire communication is carried out through the cluster heads. The clock mismatch between various nodes and clusters often leads to collisions, delay and data loss. In order to overcome this problem, a novel RTS/CTS based Relative Time Synchronization Protocol is being proposed for Radio-Frequency Identification based WSN. It achieves better performance due to its energy efficiency and lower service messages. Simulation results show a substantial improvement in the net throughput and reliability of the network when compared with the GPS-based Synchronization technique.