The disclosure is directed to systems and methods for patching computer programs. In one example, a patch is virtually installed to a computing device having a base file system and configuration, a computer program, and a patch layering subsystem. The virtual installation may include storing content of the patch to a patch layer, and generating and storing mapping data defining at least one relationship between the content in the patch layer and content in the base file system and configuration. The virtually installed patch may be enabled, including applying the mapping data to the patch layering subsystem such that the patch layering subsystem is configured for selectively redirecting access requests from the base file system and configuration to the patch layer. In certain embodiments, the enabled patch may be disabled by reversing the application of the mapping data to the patch layering subsystem.