There are three potential solutions:
Hardware Solution:
Use a free output pin on the processor and hook an oscilloscope or logic analyzer to the pin. Initialize the pin to a low state, just before calling the function you want to measure, assert the pin to a high state and just after returning from the function, deassert the pin.
*io_pin = 1;
myfunc();
*io_pin = 0;
Bookworm solution:
If the function is fairly small, and you can manage the disassembled code, you can crack open the processor architecture databook and count the cycles it will take the processor to execute every instructions. This will give you the number of cycles required.
Time = # cycles * Processor Clock Rate / Clock ticks per instructions
This is easier to do for smaller functions, or code written in assembler (for a PIC microcontroller for example)
Timestamp counter solution:
Some processors have a timestamp counter which increments at a rapid rate (every few processor clock ticks). Simply read the timestamp before and after the function.
This will give you the elapsed time, but beware that you might have to deal with the counter rollover.