A communication device for handling a Non-Access Stratum (NAS) procedure comprises instructions of transmitting a first session management (SM) message related to an access point name (APN) to a network; receiving a second SM message comprising a SM cause of insufficient resources and a back off timer value of a back off timer indicating that the back off timer is deactivated from the network in response to the transmission the first SM message; being forbidden to transmit a third SM message for the APN to the network, when the back off timer is deactivated for the APN; receiving a fourth SM message from the network indicating to deactivate and to reactivate an activated SM context associated with the APN, when the back off timer is deactivated for the APN; and transmitting a fifth SM message related to the APN to the network.