In FusionReactor by default, any transaction running for more than 3 seconds will be profiled automatically.
Note that it can take up to 1 second for the profiler to begin profiling so it could be 4 seconds rather than 3.
If you wish to profile requests after a shorter duration as your requests do not run that long or you have too many profiled requests and would like to reduce this, you can reduce modify the minimum transaction time before initializing the profiler.
You can do so in the profiler setting.