One embodiment of the present invention provides a system for performing time measurements during instrumentation-based profiling. The system operates by first measuring time required to execute instrumentation code in isolation. Next, it receives the code to be profiled (user application), inserts the instrumentation code into it, and executes this combined code. The system then measures the time it takes to execute the combined code. Finally, it subtracts the previously obtained instrumentation code execution time from the total combined code execution time, thus obtaining the exact execution time for the user application.