If Nick Fury had prior knowledge that Iron Man was coming and had time to prepare, say a couple of days, then he could probably gather all the advanced weaponry he'd need to take on Stark from the SHIELD armory.
When it comes to straight up hand to hand fighting, Fury is easily the better fighter. Fury has spent virtually his entire century long life fighting wars against foreign countries, superhuman criminals and terrorist organizations. The problem is that Fury is just an ordinary man. He ages much slower than normal humans due to the Infinity Formula but that's the only thing remotely superhuman about him.
Tony Stark's Iron Man armor is sort of the Swiss Army Knife of superhero gadgetry. He practically has a different armor for whatever circumstances pop up. Aside from the various weaponry he has in his armors, they all grant him superhuman strength, stamina and resistance to physical injury. In the various Marvel handbooks, the armor is enough to boost Tony Stark's physical strength to the 100 ton level. If he hit a normal human like Nick Fury with only a fraction of of his strength, Fury would probably explode. There'd be little left of him except for bits of mangled body tissue that the entire cast of Bones wouldn't be able to identify.
Fury is resourceful and courageous. As I said, if he had time to prepare, then he could probably get his hands on some weaponry that would give him a change. If I'm not mistaken, SHIELD has exoskeleton suits of armor similar to Tony Stark's that some of their agents wear. They're not nearly as advanced but the technology behind them is roughly the same. If Fury could get his hands on one of those and some top weaponry, then he might honestly be able to beat Stark.
However, just going one on one as is, he has virtually no chance. The old soldier goes out bravely and fighting, but he does go out. Iron Man wins this.
