Sure, you can replace the stock fan on CPU cooler. Just make sure to replace the fan with same airflow (65 CFM) and static pressure (2.1 mmH2O), or better. Since installing poorer fan will reduce the CPU cooler effectiveness.
I've also replaced the stock fan on my CPU cooler. I have Arctic Cooling Freezer i32 in use and it came with one 120mm semi-passive fan. I replaced it with two 120mm Corsair ML120 Pro red LED fans, for nicer eyecandy and considerably better cooling performance (since i'm running push-pull).
Image too (Skylake build, full specs with more pics in my sig):