A computer-implemented method for protecting virtual machine program code may include (1) identifying one or more software program functions developed for execution in a virtual machine to be protected against reverse engineering, (2) converting one or more of the software program functions to native code for the computing device, (3) obtaining a memory address of one or more virtual machine functions, (4) generating one or more at least partially random alphanumeric values to identify the memory address of the virtual machine functions, (5) invoking the converted native code using a native code interface for the virtual machine, and (6) invoking one or more of the virtual machine functions from the converted native code using the alphanumeric value. Various other methods, systems, and computer-readable media are also disclosed.