yes...
the only "problem" is that from '97-'02 they vented the tops on the back corners...and in '03 (I'm almost positive that was the first year) they moved the vent to the tailgate...
so, an '00 top on an '03 would be double-vented...while an '03 top on an '00 TJ would not have any vents...
but, it will fit...
it may never be a problem...but you may get excessive window fogging in cold weather a good pressure build up when you slam a door...
Greg