An apparatus for controlling platooning controls timing of transmitting or receiving a message. The apparatus includes a communication device to communicate with other vehicles in a platoon and to transmit a message, which is received from the other vehicles, in a form of a full message and includes a controller to generate logic message for the platooning, to check omission of the message from the full message received using the communication device, and to adjust a latency of the message when the omission of the message occurs.