I have a 2000 cherokee sport and it seems to have a loud "flutter" or "click" in the front end (seems to be on the other side of the firewall in the center of the vehicle) whenever I go over a substantial bump. More recently, this "flutter"/"click" has begun occurring when I brake on a hard stop - when I release the brake it stops and then starts again if I press the brake hard. I have looked underneath the vehicle and the only thing that seems to be under where the noise is coming from is the transfer case. Any ideas? I am stumped. . .

 

when does it click ?

 

if it's a constant click that will go on for a couple seconds then stop and it has a somewhat squeaky noise to it my 98 cherokee does the same thing. If it's not that it might be a wire or connector under your hood that is just tapping on the firewall. (I'm not an expert im just giving my personal opinion)

 

that sounds exactly like what happened to my 90 just before my ring gear blew out. i still havent replaced the axle yet i just removed the u joints and pulled my axle shafts out. i only have 2wd but its driveable n i have the winch in case i get in a messy situation. not that ive needed it yet. its unstoppable even in 2 wheel.

 

I had a loud clicking/flutter on my 2001 Xj, loud enough that I wasn't sure where it was coming from. Hopefully it's not from your t-case. It's probably something rubbing up against a rotary part.
Check for anything loose around your radiator fan. The hood release cables on mine were hanging low enough to hit the fan when I went over bumps. The plastic clips where missing, fixed it with some zip ties in five minutes.