Yes. It's mounted using a bracket on the rear of the motherboard, so unless you have a large cutout in your motherboard tray you'll have to take it out.
To be honest though, those motherboard cutouts I think just foster lazy behaviour - if you care about your hardware you'll want to make sure your cooler is properly mounted, so why take shortcuts and mount a cooler while the motherboard is still in the case?
ALWAYS take the board out; it'll save you hassle and time in the long run.
Thanks for the information. The guts of my computer are housed in the cooler master 942 HAF X which has a very large cut out behind the cpu. So I just might be able to get the cooler in without taking the board out. If not then I will certainly follow your advice