The present invention relates to a method and system of secure wakeup in a communication system. The method comprises: transmitting a predetermined wakeup code by a wakeup transmitter of a first node to a wakeup receiver of a second node using a first communication link; establishing a protocol for future wakeup codes periodically between the first node and the second node using a second communication link; wherein the wakeup code is updated based on at least one of: the protocol for future wakeup codes, a first function of time defined by protocol for future wakeup codes, a second function of number of wakeups defined by protocol for future wakeup codes; comparing the wakeup code received by the second node with the wakeup code sent by the first node; and if the wakeup code received by the second node matches a template wakeup code derived from a protocol for future wakeup codes, then the receiver wakes up; otherwise the receiver does not wakeup.