A system and method for evaluating performance of a software application. The present invention includes analyzing by one or more computing devices a plurality of program code lines of the software application stored in one or more computer databases. Further, one or more equivalent program regions within the plurality of program code lines may be identified. One or more markers in the identified one or more equivalent program regions may be inserted and stored in the one or more computer databases. Further, the plurality of program code lines may be compiled and assembled respectively to generate an executable code. The executable code may include a plurality of instructions. Further, performance metrics of the software application may be measured by manipulating the plurality of instructions based on the one or more equivalent program regions identified by the inserted one or more markers and executing the executable code.