The two systems are substantially similar. Both use a linear distribution die, both use HP, both use fairly similar stats (Seriously, IIRC, Nyarlahotep has a Dexterity of 19 in BRP), the sanity system is identical.
The few differences might matter to you in play, and they might not. BRP has no feats, of course, and has a roll-under percentile skill system. That's easy to learn but takes away some character differentiation and simulation ability. IME, speed of resolution in play is about the same. People have the impression, from D&D, the d20 combat takes forever. This mostly doesn't carry over, because normally you don't have interative attacks or rampant spellcasting in CoC.
Finally, the DM advice in the d20 version is fantastic. It's worth the price of the book on that alone, IMO. Also, as Joe suggests, if you want Cthuloid beasties and sanity-blasting magic premade to drop into your D&D game, d20 CoC will give it to you.
I own and like both, but when I run I prefer d20 because my players hate learning new systems.
Cheers.