Provided is a method and system for code obfuscation of an application. A method configured as a computer may include receiving an application program package that includes an intermediate language (IL) code generated by compiling code for an application including a plurality of classes and a plurality of methods as a dex file over a network, selecting a protection target class or a protection target method from among the plurality of classes and the plurality of methods, encrypting the selected protection target class or the selected protection target method by retrieving and encrypting an IL code corresponding to the selected protection target class or the selected protection target method from the dex file, and adding decryption information for decrypting the encrypted protection target class or the encrypted protection target method to a secure module that is further included in the application program package.