Provided are a method and an apparatus for performing a HARQ based on a polar code in a wireless communication system. The apparatus transmits multiple first output bits, which are generated from multiple first input bits, to a receiver. Upon receiving a retransmission request, the apparatus generates multiple second output bits from multiple second input bits. The apparatus selects multiple third output bits from among the multiple second output bits, and transmits the selected multiple third output bits to the receiver. Bits, which are encoded differently from the multiple first output bits among the multiple second output bits, are preferentially selected as the multiple third output bits.