A method and an apparatus of protecting binary data stored in non-volatile memory are disclosed herein. The apparatus for protecting binary data in non-volatile memory includes a reception unit, a detection unit, a generation unit, an encryption unit, and a storage unit. The reception unit receives program code. The detection unit detects the binary pattern of binary data constituting the program code by analyzing the received program code. The generation unit generates unique pattern information corresponding to the binary pattern based on the detected binary pattern. The encryption unit encrypts the program code using the generated unique pattern information as a key value. The storage unit stores the encrypted program code in memory.