An implantable medical device includes a local clock generator for generating a system clock signal. The local clock generator is periodically calibrated to maintain accuracy of the generated system clock signal. A clocking circuit is coupled to the local clock generator to provide the calibration factor for calibrating the local clock generator. The implantable medical device receives an accurate clock signal that is transmitted from an external device and the accurate clock signal is provided to the clocking circuit. The system clock signal is also provided to the clocking circuit and a computation is performed to derive the calibration factor.