A first base station (BS) for handling a handover with a second BS comprises a storage unit for storing instructions and a processing circuit coupled to the storage unit. The processing circuit is configured to execute the instructions stored in the storage unit. The instructions comprise determining to hand over a first communication device to the second BS; generating a first handover request message, wherein the first handover request message comprises one of first system information and second system information according to whether the first communication device is in coverage enhancement (CE) or according to a type of the first communication device; transmitting the first handover request message to the second BS; receiving a first handover request acknowledgement message from the second BS; and transmitting a first handover command to the first communication device in response to the reception of the first handover request acknowledgement message.