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Implantable sensor network becomes nowadays an important area of research. Sensors are implanted inside the patient body to measure its physiological changes and send them wirelessly to an external close-by device. Such network is called IWBSN (Implantable Wireless Body Sensor Network). The life time of the embedded batteries associated with these tiny sensor nodes is too short. Hence power consumption is the most important design metrics associated with these sensors. A novel ultra low energy communication protocol has been proposed to address the life time of the battery within the sensor. Our proposed protocol is based on time synchronization between all sensor nodes and the base station, where the delay of the wireless signal propagation is very critical. Tracking of the time synchronization using the standard algorithms is very costly energy-wise. In this paper, we propose a technique which automatically calculates the delay (sensor-node to Base-station) and compensates for any discrepancies. This correction is done while saving the tiny energy resources inside the sensor nodes. Our proposed solution has been tested wirelessly through transceiver boards using a single FPGA board. The experimental results have shown the correctness of our protocol along with the delay correction technique.