Provided are a method of configuring a protocol header in a wireless communication system, and a communication apparatus and method using the protocol header configuration method. The protocol header configuration method may include: configuring a variable length physical layer (PHY) header and a fixed length PHY header; encoding the fixed length PHY header according to a first coding scheme; generating a Header Check Sequence (HCS) to check an error regarding a combination of the fixed length PHY header, the variable length PHY header, and a Media Access Control (MAC) header; scrambling the MAC header and an HCS to generate a scrambled MAC header and HCS; and encoding the variable length PHY header and the scrambled MAC header and HCS according to a second coding scheme.