The easiest solution is to test your program in Wabbitemu without the skin enabled. You should then see Wabbitemu's built-in FPS feature on the bottom of the window, which should be accurate for any Axe program. (It may not be accurate for assembly programs with custom screen updating methods, but you don't need to worry about that)
However, if you need an actual FPS counter built into your program, I would suggest using interrupts in your program and using them to keep track of and display an approximate FPS.